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Species
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Short Read Archive
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Short Read Archive
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Experiment
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Experimental Design
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Sequencing Details
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Sequence File
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References
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Project Number
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Accession Number
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Location
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Taxus mairei
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SRX5446617
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SRR8648837
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leaves
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individual trees of JXS and WT were analyzed by RNA-seq to describe the transcriptome and reveal transcriptome profiles in the present study. This is the first study to illustrate the taxol synthesis pathway based on the transcriptome profile of a new cultivar of T. mairei with a high taxol content in the needles
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source tissue needles; triplicates of each variety pooled; enriched mRNA via oligo (dT) beads; paired-end sequencing
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Taxus mairei ssp.
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SRX5446616
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SRR8648838
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leaves
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individual trees of JXS and WT were analyzed by RNA-seq to describe the transcriptome and reveal transcriptome profiles in the present study. This is the first study to illustrate the taxol synthesis pathway based on the transcriptome profile of a new cultivar of T. mairei with a high taxol content in the needles
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source tissue needles; triplicates of each variety pooled; enriched mRNA via oligo (dT) beads; paired-end sequencing
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Taxus mairei rep3
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SRX4907221
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SRR8080082
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GSM3438658: Taxus mairei rep3; Taxus mairei; RNA-Seq
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comparative analysis of the transcriptomes in three Taxus species. KEGG enrichment analysis revealed the diterpenoid biosynthesis and cytochrome P450 pathways were significantly enriched in different comparisons. 48 JA-related transcription factor (TF) genes, including 10 MYBs, 5 ERFs, 4 RAPs, 3 VTCs, and 26 other TFs, were analyzed. Differential expression of these JA-related TF genes suggested distinct responses to exogenous JA applications in the three Taxus species.
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source tissue fresh three-year old twigs; triplicates of each variety; enriched mRNA via olgio (dT) beads;
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Taxus mairei rep2
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SRX4907220
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SRR8080081
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GSM3438657: Taxus mairei rep2; Taxus mairei; RNA-Seq
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comparative analysis of the transcriptomes in three Taxus species. KEGG enrichment analysis revealed the diterpenoid biosynthesis and cytochrome P450 pathways were significantly enriched in different comparisons. 48 JA-related transcription factor (TF) genes, including 10 MYBs, 5 ERFs, 4 RAPs, 3 VTCs, and 26 other TFs, were analyzed. Differential expression of these JA-related TF genes suggested distinct responses to exogenous JA applications in the three Taxus species.
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source tissue fresh three-year old twigs; triplicates of each variety; enriched mRNA via olgio (dT) beads;
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Taxus mairei rep1
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SRX4907219
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SRR8080080
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GSM3438656: Taxus mairei rep1; Taxus mairei; RNA-Seq
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comparative analysis of the transcriptomes in three Taxus species. KEGG enrichment analysis revealed the diterpenoid biosynthesis and cytochrome P450 pathways were significantly enriched in different comparisons. 48 JA-related transcription factor (TF) genes, including 10 MYBs, 5 ERFs, 4 RAPs, 3 VTCs, and 26 other TFs, were analyzed. Differential expression of these JA-related TF genes suggested distinct responses to exogenous JA applications in the three Taxus species.
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source tissue fresh three-year old twigs; triplicates of each variety; enriched mRNA via olgio (dT) beads;
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Taxus mairei
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SRX179290
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SRR797069
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degradome sequencing library
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To elucidate the role of miRNAs in Taxus a deep sequencing approach to analyze the small RNA and degradome sequence tags of Taxus mairei leaves was used. The novel miRNA m0034 turns out to be from the intron sequence of the paclitaxel biosynthetic gene taxadiene synthase. It is found that two paclitaxel biosynthetic genes, taxane 13α hydroxylase and taxane 2α‐O‐benzoyltransferase, are the cleavage targets of miR164 and miR171, respectively. This study represents the first transcriptome‐based analysis of miRNAs and degradome in gymnosperms.
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source tissue fresh leaves; RNA fragments of 18–30 nucleotides (nts) isolated
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Taxus mairei
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SRX179289
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SRR797042
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sRNA sequencing library
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To elucidate the role of miRNAs in Taxus a deep sequencing approach to analyze the small RNA and degradome sequence tags of Taxus mairei leaves was used. The novel miRNA m0034 turns out to be from the intron sequence of the paclitaxel biosynthetic gene taxadiene synthase. It is found that two paclitaxel biosynthetic genes, taxane 13α hydroxylase and taxane 2α‐O‐benzoyltransferase, are the cleavage targets of miR164 and miR171, respectively. This study represents the first transcriptome‐based analysis of miRNAs and degradome in gymnosperms.
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source tissue fresh leaves; RNA fragments of 18–30 nucleotides (nts) isolated
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Taxus mairei
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SRX170671
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SRR527088
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Taxus chinensis transcriptome
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De novo transcriptome assembly of the Taxus chinensis var. mairei transcriptome. Illumina GA reads were assembled using SOAPdenovo ver 3.2
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Taxus mairei
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SRX037161
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SRR350861
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DGE results of Taxus mairei
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de novo assembly of Taxus mairei transcriptome using Illumina paired-end sequencing; investigation of the transcriptome difference of three Taxus tissues using a tag-based digital gene expression system was employed; The expression of the taxane biosynthetic genes is significantly higher in the root than in the leaf and the stem, while high activity of taxane-producing pathway in the root was also revealed via metabolomic analyses. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and enriched metabolic pathways with regard to the differentially expressed genes were revealed for the first time.
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Taxus mairei
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SRX037160
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SRR350719
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RNA-seq results of Taxus mairei
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de novo assembly of Taxus mairei transcriptome using Illumina paired-end sequencing; investigation of the transcriptome difference of three Taxus tissues using a tag-based digital gene expression system was employed; The expression of the taxane biosynthetic genes is significantly higher in the root than in the leaf and the stem, while high activity of taxane-producing pathway in the root was also revealed via metabolomic analyses. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and enriched metabolic pathways with regard to the differentially expressed genes were revealed for the first time.
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Taxus baccata
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SRX2999991
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SRR5822140
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De novo assembly and comparative study of English yew (Taxus baccata) transcriptome.
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De novo assembly and comparative study of English yew (Taxus baccata) transcriptome. Study identified orthologs, tested phylogenomic relationships and detected genes potentially involved in the evolutionary adaptation of the genus worldwide.
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Random sequencing of whole transcriptome
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Taxus baccata
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SRX2999990
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SRR5822141
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De novo assembly and comparative study of English yew (Taxus baccata) transcriptome.
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De novo assembly and comparative study of English yew (Taxus baccata) transcriptome. Study identified orthologs, tested phylogenomic relationships and detected genes potentially involved in the evolutionary adaptation of the genus worldwide.
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Random sequencing of whole transcriptome
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Taxus baccata
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ERX337175
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ERR364406
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Population Genomics of English yew
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1KP is an international multidisciplinary consortium acquiring large-scale gene sequences for the Viridiplantae (green plants), incorporating at some phylogenetic/taxonomic level nearly all known species from angiosperms to algae. This pilot study is the first 85 species of the >1000 species to be sequenced.
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Taxus baccata
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ERX242665
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ERR268425
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Illumina PE sequencing of an english yew mature needles sample
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Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon revealed that the TE diversity is shared among extant conifers. Expression of 24nt sRNAs, previously implicated in TE silencing, was tissue-specific and much lower than in other plants. We further identified numerous long (>10,000 bp) introns, gene like fragments, uncharacterized long non- coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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Whole genome sequencing of Taxus baccata (English Yew) to construct a draft genome assembly.
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Taxus baccata
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ERX242665
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ERR268426
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Illumina PE sequencing of an english yew mature needles sample
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Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon revealed that the TE diversity is shared among extant conifers. Expression of 24nt sRNAs, previously implicated in TE silencing, was tissue-specific and much lower than in other plants. We further identified numerous long (>10,000 bp) introns, gene like fragments, uncharacterized long non- coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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Whole genome sequencing of Taxus baccata (English Yew) to construct a draft genome assembly.
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Taxus baccata
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ERX242665
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ERR268427
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Illumina PE sequencing of an english yew mature needles sample
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Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon revealed that the TE diversity is shared among extant conifers. Expression of 24nt sRNAs, previously implicated in TE silencing, was tissue-specific and much lower than in other plants. We further identified numerous long (>10,000 bp) introns, gene like fragments, uncharacterized long non- coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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Whole genome sequencing of Taxus baccata (English Yew) to construct a draft genome assembly.
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Taxus baccata
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ERX242664
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ERR268424
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454 sequencing of an english yew mature needles sample
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Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon revealed that the TE diversity is shared among extant conifers. Expression of 24nt sRNAs, previously implicated in TE silencing, was tissue-specific and much lower than in other plants. We further identified numerous long (>10,000 bp) introns, gene like fragments, uncharacterized long non- coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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Whole genome sequencing of Taxus baccata (English Yew) to construct a draft genome assembly.
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Taxus baccata
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SRX026383
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SRR065067
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454 sequencing of Taxus baccata EST project
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DOE Joint Genome Institute Taxus baccata EST project
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Taxus brevifolia Plastome 01
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MH390457.1
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MH390457.1
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Taxus brevifolia isolate 01 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus brevifolia Plastome 02
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MH390484.1
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MH390484.1
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Taxus brevifolia isolate 02 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus brevifolia Plastome 03
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MH390459.1
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MH390459.1
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Taxus brevifolia isolate 03 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus calcicola Plastome 01
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MH390451.1
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MH390451
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Taxus calcicola isolate 01 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus calcicola Plastome 02
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MH390461.1
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MH390461.1
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Taxus calcicola isolate 02 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus calcicola Plastome 03
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MH390489.1
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MH390489.1
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Taxus calcicola isolate 03 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus canadensis Plastome 01
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MH390483.1
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MH390483.1
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Taxus canadensis isolate 01 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus canadensis Plastome 02
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MH390448.1
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MH390448.1
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Taxus canadensis isolate 02 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus canadensis Plastome 03
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MH390466.1
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MH390466.1
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Taxus canadensis isolate 03 chloroplast, complete genome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus chinensis P60
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SRX7082461
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SRR10381647
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Taxus chinensis Raw sequence reads
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The Taxus chinensis regeneration tissues RNA-seq data for different time after bark girdling
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samples collected 60 days after bark girdling
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Taxus chinensis P18
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SRX7082460
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SRR10381648
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Taxus chinensis Raw sequence reads
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The Taxus chinensis regeneration tissues RNA-seq data for different time after bark girdling
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samples collected 18 days after bark girdling
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Taxus chinensis P12
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SRX7082459
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SRR10381649
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Taxus chinensis Raw sequence reads
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The Taxus chinensis regeneration tissues RNA-seq data for different time after bark girdling
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samples collected 12 days after bark girdling
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Taxus chinensis P06
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SRX7082458
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SRR10381650
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Taxus chinensis Raw sequence reads
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The Taxus chinensis regeneration tissues RNA-seq data for different time after bark girdling
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samples collected 6 days after bark girdling
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Taxus chinensis P00
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SRX7082457
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SRR10381651
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Taxus chinensis Raw sequence reads
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The Taxus chinensis regeneration tissues RNA-seq data for different time after bark girdling
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samples collected 0 day after bark girdling
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Taxus chinensis
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SRX3059901
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Gymnosperms transcriptome
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study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis.
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Taxus chinensis CA
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SRX573749
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SRR1343578
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raw reads of miRNA in NA and CA
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The overexpression of these miRNAs in CA increased the genes of taxol, phenylpropanoid, and flavonoid biosynthesis, thereby suggesting their function as crucial factors that regulate the entire metabolic network during long-term subculture. Our current studies indicated that a positive conversion of production properties from secondary metabolism to primary metabolism occurred in long-term subcultured cells. miRNAs are important regulators in the upregulation of primary metabolism.
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two Taxus cell lines, CA (sub-cultured for 10 years) and NA (fresh separated and sub-cultured for 6 months) were quantified at both mRNA and miRNA levels by high-throughput sequencing, looking forward to clarify the regulation mechanisms of cell degeneration.
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Taxus chinensis CA # 48
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SRX571877
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SRR1339474
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mRNA-seq of CA
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CA cell line was T. chinensis cell line #48 established from callus cultures derived from initiated embryos excised from leaves in May 2003
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two Taxus cell lines, CA (sub-cultured for 10 years) and NA (fresh separated and sub-cultured for 6 months) were quantified at both mRNA and miRNA levels by high-throughput sequencing, looking forward to clarify the regulation mechanisms of cell degeneration.
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Taxus chinensis CA # 48
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SRX571877
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SRR1343576
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mRNA-seq of CA
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CA cell line was T. chinensis cell line #48 established from callus cultures derived from initiated embryos excised from leaves in May 2004
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two Taxus cell lines, CA (sub-cultured for 10 years) and NA (fresh separated and sub-cultured for 6 months) were quantified at both mRNA and miRNA levels by high-throughput sequencing, looking forward to clarify the regulation mechanisms of cell degeneration.
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Taxus chinensis NA
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SRX571875
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SRR1339463
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mRNA-seq of NA
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NA cell line was established from callus cultures newly derived from initiated embryos excised from leaves in May 2013 and maintained for 6 months before RNA extraction
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two Taxus cell lines, CA (sub-cultured for 10 years) and NA (fresh separated and sub-cultured for 6 months) were quantified at both mRNA and miRNA levels by high-throughput sequencing, looking forward to clarify the regulation mechanisms of cell degeneration.
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Taxus chinensis NA
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SRX571875
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SRR1343572
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mRNA-seq of NA
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NA cell line was established from callus cultures newly derived from initiated embryos excised from leaves in May 2013 and maintained for 6 months before RNA extraction
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two Taxus cell lines, CA (sub-cultured for 10 years) and NA (fresh separated and sub-cultured for 6 months) were quantified at both mRNA and miRNA levels by high-throughput sequencing, looking forward to clarify the regulation mechanisms of cell degeneration.
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Taxus contorta
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NC_041497.1
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NC_041497.1
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Taxus contorta Plastome
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus floridana Plastome
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NC_041505.1
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NC_041505.1
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Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide
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Taxus floridana Plastome
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SRX5546198
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SRR8755471
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ddRAD-seq of Taxus florinii:TFP030307
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX5546197
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SRR8755472
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ddRAD-seq of Taxus florinii:TFP030208
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX2763417
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SRR5479591
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ddRAD-seq of Taxus florinii: TFP030101
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX2763416
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SRR5479590
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ddRAD-seq of Taxus florinii: TFP030103
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX2763415
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SRR5479589
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ddRAD-seq of Taxus florinii: TFP030104
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX2763414
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SRR5479588
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ddRAD-seq of Taxus florinii: TFP030108
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX2763413
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SRR5479587
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ddRAD-seq of Taxus florinii: TFP030202
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX2763412
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SRR5479586
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ddRAD-seq of Taxus florinii: TFP030205
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
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SRX2763411
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SRR5479585
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ddRAD-seq of Taxus florinii: TFP030206
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In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
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Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
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Taxus floridana Plastome
|
SRX2763410
|
SRR5479584
|
ddRAD-seq of Taxus florinii: TFP030208
|
In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
|
Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
|
||
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Taxus floridana Plastome
|
SRX2763409
|
SRR5479583
|
ddRAD-seq of Taxus florinii: TFP030304
|
In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
|
Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
|
||
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Taxus floridana Plastome
|
SRX2763408
|
SRR5479582
|
ddRAD-seq of Taxus florinii: TFP030307
|
In this study, MiddRAD-seq data was used to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. The total number of alleles per locus ranged from two to ten (mean = 4.875), and within-population expected heterozygosity from zero to 0.789 (mean = 0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.
|
Ten individuals from T. florinii population TFP03 were used to build a MiddRAD library. In addition, twelve individuals of this population and twelve from population TFP04 were selected for validating microsatellite polymorphism.
|
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Taxus globosa Plastome 05
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NC_041500.1
|
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Taxus globosa isolate 05 chloroplast, complete genome
|
N/A
|
|
||
|
Taxus yunnanensis
|
SRX3520672
|
SRR6428981
|
Taxus yunnanensis sequencing
|
High 10-DAB III content was identified in the needle of T. yunnanensis cultivar Zd2. Transcriptome analysis of different tissues of Zd2 provided the understanding of tissues specific expression pattern of taxol biosynthesis.
|
The plants of the cultivar Zd2 for branch and needle sampling were of the same age as cultivar Zd1 and WT (21 years old), and the samples of the three experimental lines were collected at the same time. The plants of the three experimental lines were grown at the same site under the same growth conditions; Two-year branches with fresh needles of T. yunnanensis WT, Zd1, and Zd2 were collected; The needles appeared at the same stage were stripped off from the collected branches to determine paclitaxel and 10-DAB III contents separately; root samples of these three experimental lines were collected from nursery plant (2 years old).
|
||
|
Taxus yunnanensis
|
SRX3520671
|
SRR6428982
|
Taxus yunnanensis sequencing
|
High 10-DAB III content was identified in the needle of T. yunnanensis cultivar Zd2. Transcriptome analysis of different tissues of Zd2 provided the understanding of tissues specific expression pattern of taxol biosynthesis.
|
The plants of the cultivar Zd2 for branch and needle sampling were of the same age as cultivar Zd1 and WT (21 years old), and the samples of the three experimental lines were collected at the same time. The plants of the three experimental lines were grown at the same site under the same growth conditions; Two-year branches with fresh needles of T. yunnanensis WT, Zd1, and Zd2 were collected; The needles appeared at the same stage were stripped off from the collected branches to determine paclitaxel and 10-DAB III contents separately; root samples of these three experimental lines were collected from nursery plant (2 years old).
|
||
|
Taxus yunnanensis
|
SRX3520670
|
SRR6428983
|
Taxus yunnanensis sequencing
|
High 10-DAB III content was identified in the needle of T. yunnanensis cultivar Zd2. Transcriptome analysis of different tissues of Zd2 provided the understanding of tissues specific expression pattern of taxol biosynthesis.
|
The plants of the cultivar Zd2 for branch and needle sampling were of the same age as cultivar Zd1 and WT (21 years old), and the samples of the three experimental lines were collected at the same time. The plants of the three experimental lines were grown at the same site under the same growth conditions; Two-year branches with fresh needles of T. yunnanensis WT, Zd1, and Zd2 were collected; The needles appeared at the same stage were stripped off from the collected branches to determine paclitaxel and 10-DAB III contents separately; root samples of these three experimental lines were collected from nursery plant (2 years old).
|
||
|
T_wallichiana
|
SRX1176252
|
|
three tissues of mutant and wildtype of taxus yunnanensis
|
The significant negative correlations between differential expressed TFs and DEGs from paclitaxel biosynthesis pathway displayed a possibly negative regulation pattern of these TFs on paclitaxel biosynthesis pathway genes. These results provided new insights into the molecular process of paclitaxel synthesis in Taxus.
|
Needle samples of WT and ZD1 were simultaneously collected; needles, branches and root samples of WT and ZD1 with the same age (21-year-old) grown under the same cultivating conditions were collected independently.
|
|
|
|
Taxus media var. hicksii
|
SRR10854762
|
SRX7525164
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
flg22_t2_B2T2 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854763
|
SRX7525163
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
Initial_t0_B2T2 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854764
|
SRX7525162
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
MeJa_t2_B2T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854765
|
SRX7525161
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
Chi_t14_B2T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854766
|
SRX7525160
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
Initial_t0_B2T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854767
|
SRX7525159
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
Chi_t2_B1T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854768
|
SRX7525158
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
VS_t2_B2T2 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854769
|
SRX7525157
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
flg22_t2_B1T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854770
|
SRX7525156
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
flg22_t2_B2T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854771
|
SRX7525155
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
flg22_t14_B2T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854772
|
SRX7525154
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
flg22_t14_B2T2 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854773
|
SRX7525153
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
Chi_t2_B2T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854774
|
SRX7525152
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
VS_t2_B2T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854775
|
SRX7525151
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
NegChi_t2_B2T2 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854776
|
SRX7525150
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
VS_t14_B1T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854777
|
SRX7525149
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
Chi_t2_B1T2 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854778
|
SRX7525148
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
VS_t14_B1T2 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854779
|
SRX7525147
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
VS_t14_B2T2 transcriptome
|
|
|
| Taxus media var. hicksii |
SRR10854780
|
SRX7525146
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
flg22_t14_B1T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854781
|
SRX7525145
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
NegMeJa_t2_B1T1 transcriptome
|
|
|
|
Taxus media var. hicksii
|
SRR10854782
|
SRX7525144
|
expression profiling
|
Exploring the G3 Gymnosperm Giga-Genomes" for Carbon Sequestration
|
flg22_t14_B1T2 transcriptome
|
|
|
|
Taxus media
|
SRX4910268
|
SRR8083193
|
Degradome of Callus
|
Multi-omics analysis was employed to detect the reprogramming transcriptional profiles, attempt to reveal the key pathways responding to these changes, and finally intend to clarify the regulation mechanisms.
|
Approximately 20 ug of total RNA were used to prepare Degradome library. The method differed considerably from past efforts (Addo-Quaye et al., 2008, 2009b) and followed as (Maet al., 2010) with some modification.
|
|
|
|
Taxus media
|
SRX4910267
|
SRR8083194
|
Degradome of Tissues
|
Multi-omics analysis was employed to detect the reprogramming transcriptional profiles, attempt to reveal the key pathways responding to these changes, and finally intend to clarify the regulation mechanisms.
|
Approximately 20 ug of total RNA were used to prepare Degradome library. The method differed considerably from past efforts (Addo-Quaye et al., 2008, 2009b) and followed as (Maet al., 2010) with some modification.
|
|
|
|
Taxus media
|
SRX4910266
|
SRR8083195
|
transcriptome of Callus
|
Multi-omics analysis was employed to detect the reprogramming transcriptional profiles, attempt to reveal the key pathways responding to these changes, and finally intend to clarify the regulation mechanisms.
|
Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen).
|
|
|
|
Taxus media
|
SRX4910265
|
SRR8083196
|
transcriptome of Tissue
|
Multi-omics analysis was employed to detect the reprogramming transcriptional profiles, attempt to reveal the key pathways responding to these changes, and finally intend to clarify the regulation mechanisms.
|
Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen).
|
|
|
|
Taxus media
|
SRX4910264
|
SRR8083197
|
miRNA-seq of Calli1
|
Multi-omics analysis was employed to detect the reprogramming transcriptional profiles, attempt to reveal the key pathways responding to these changes, and finally intend to clarify the regulation mechanisms.
|
Library construction followed as the instruction of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)
|
|
|
|
Taxus media
|
SRX4910263
|
SRR8083198
|
miRNA-seq of Tissue1
|
Multi-omics analysis was employed to detect the reprogramming transcriptional profiles, attempt to reveal the key pathways responding to these changes, and finally intend to clarify the regulation mechanisms.
|
Library construction followed as the instruction of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)
|
|
|
|
Taxus media rep 3
|
SRX4907227
|
SRR8080088
|
GSM3438664: Taxus media rep3; Taxus x media; RNA-Seq
|
Variations in the expression pattern and sequence similarity of the key genes involved in the metabolism of taxoids among three Taxus species
|
Fresh twig samples were harvested from three-year-old cultivated Taxus trees, including T. media, T. mairei, and T. cuspidata. Five independent trees for each species were used in our study.
|
||
|
Taxus media rep 2
|
SRX4907226
|
SRR8080087
|
GSM3438663: Taxus media rep2; Taxus x media; RNA-Seq
|
Variations in the expression pattern and sequence similarity of the key genes involved in the metabolism of taxoids among three Taxus species
|
Fresh twig samples were harvested from three-year-old cultivated Taxus trees, including T. media, T. mairei, and T. cuspidata. Five independent trees for each species were used in our study.
|
||
|
Taxus media rep 1
|
SRX4907225
|
SRR8080086
|
GSM3438662: Taxus media rep1; Taxus x media; RNA-Seq
|
Variations in the expression pattern and sequence similarity of the key genes involved in the metabolism of taxoids among three Taxus species
|
Fresh twig samples were harvested from three-year-old cultivated Taxus trees, including T. media, T. mairei, and T. cuspidata. Five independent trees for each species were used in our study.
|
||
|
Taxus x media_MeJA_1_0h
|
SRX3762814
|
SRR6804108
|
Taxus media RNA-Seq DGE Data of Tm_MeJA_0h
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus x media_MeJA_2_0h
|
RX3762813
|
SRR6804109
|
Taxus media RNA-Seq DGE Data of Tm_MeJA_0h
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus x media_MeJA_3_0h
|
SRX3762812
|
SRR6804110
|
Taxus media RNA-Seq DGE Data of Tm_MeJA_0h
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_Z14
|
SRX3762721
|
SRR6804017
|
Taxus media RNA-Seq Transcriptome Data
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_2_0h
|
SRX3761909
|
SRR6803194
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_2_30m
|
SRX3761908
|
SRR6803195
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_3_3h
|
SRX3761907
|
SRR6803196
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_3_24h
|
SRX3761906
|
SRR6803197
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_2_3h
|
SRX3761905
|
SRR6803198
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_2_24h
|
SRX3761904
|
SRR6803199
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_1_0h
|
SRX3761903
|
SRR6803200
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_1_30m
|
SRX3761902
|
SRR6803201
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_1_3h
|
SRX3761901
|
SRR6803202
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_1_24h
|
SRX3761900
|
SRR6803203
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_3_0h
|
SRX3761899
|
SRR6803204
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus media_MeJA_3_30m
|
SRX3761898
|
SRR6803205
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Tm_MeJA_1_0h
|
SRX3751063
|
SRR6791873
|
RNA-Seq of Taxus media cells
|
Variation in transcriptome expression from time course MeJA treatment over 24 hours.
|
total RNA of Taxus × media cells cultured in liquid medium was extracted after 0, 0.5, 3, and 24 hours of methyl jasmonate treatment. Three biological independent repetitions were performed. The 12 extracted RNA samples were integrated and sequenced on an Illumina HiSeq 2500 platform using the pair-end method.
|
||
|
Taxus_x_media_MeJA_18h
|
SRX2069342
|
SRR4102050
|
Taxus x media MeJA elicited 18 hours RNAseq
|
Variation in transcriptome expression from time course MeJA treatment over 18 hours
|
Taxus x media 'Hicksii' cell cultures were elicited with methyl jasmonate and sampled at 0, 1, 2, 3, 4, and 18 hours. RNA was extracted from samples and sequenced on an Illumina GAIIx instrument.
|
|
|
|
Taxus_x_media_MeJA_4h
|
SRX2069341
|
SRR4102049
|
Taxus x media MeJA elicited 4 hours RNAseq
|
Variation in transcriptome expression from time course MeJA treatment over 18 hours
|
Taxus x media 'Hicksii' cell cultures were elicited with methyl jasmonate and sampled at 0, 1, 2, 3, 4, and 18 hours. RNA was extracted from samples and sequenced on an Illumina GAIIx instrument.
|
|
|
|
Taxus_x_media_MeJA_3h
|
SRX2069340
|
SRR4102048
|
Taxus x media MeJA elicited 3 hours RNAseq
|
Variation in transcriptome expression from time course MeJA treatment over 18 hours
|
Taxus x media 'Hicksii' cell cultures were elicited with methyl jasmonate and sampled at 0, 1, 2, 3, 4, and 18 hours. RNA was extracted from samples and sequenced on an Illumina GAIIx instrument.
|
|
|
|
Taxus_x_media_MeJA_2h
|
SRX2069339
|
SRR4102047
|
Taxus x media MeJA elicited 2 hours RNAseq
|
Variation in transcriptome expression from time course MeJA treatment over 18 hours
|
Taxus x media 'Hicksii' cell cultures were elicited with methyl jasmonate and sampled at 0, 1, 2, 3, 4, and 18 hours. RNA was extracted from samples and sequenced on an Illumina GAIIx instrument.
|
|
|
|
Taxus_x_media_MeJA_1h
|
SRX2069338
|
SRR4102046
|
Taxus x media MeJA elicited 1 hours RNAseq
|
Variation in transcriptome expression from time course MeJA treatment over 18 hours
|
Taxus x media 'Hicksii' cell cultures were elicited with methyl jasmonate and sampled at 0, 1, 2, 3, 4, and 18 hours. RNA was extracted from samples and sequenced on an Illumina GAIIx instrument.
|
|
|
|
Taxus_x_media_MeJA_0h
|
SRX2069337
|
SRR4102045
|
Taxus x media MeJA elicited 0 hours RNAseq
|
Variation in transcriptome expression from time course MeJA treatment over 18 hours
|
Taxus x media 'Hicksii' cell cultures were elicited with methyl jasmonate and sampled at 0, 1, 2, 3, 4, and 18 hours. RNA was extracted from samples and sequenced on an Illumina GAIIx instrument.
|
|
|
|
Control Sample Taxus x media
|
SRX156706
|
SRR534003
|
Transcriptome of nonelicited Taxus x media cells
|
Variation in transcriptome expression MeJA treatment
|
Taxus x media cell cultures were elicited with methyl jasmonate .
|
|
|
|
Methyl jasmonate treatment Taxus x media
|
SRX156707
|
SRR534004
|
transcriptome of elicted Taxus x media cells
|
Variation in transcriptome expression MeJA treatment
|
Taxus x media cell cultures were elicited with methyl jasmonate .
|
|
|
|
Trinity_A. argotaenia3
|
SRX4939854
|
SRR8113475
|
GSM3447569: Trinity_A. argotaenia3; Amentotaxus argotaenia; RNA-Seq
|
Transcriptomic analysis revealed the mechanisms involved in the differential accumulation of taxoids, flavonoids and hormones among three Taxaceae trees
|
|
|
|
|
Trinity_A. argotaenia2
|
SRX4939853
|
SRR8113474
|
GSM3447568: Trinity_A. argotaenia2; Amentotaxus argotaenia; RNA-Seq
|
Transcriptomic analysis revealed the mechanisms involved in the differential accumulation of taxoids, flavonoids and hormones among three Taxaceae trees
|
|
|
|
|
Trinity_A. argotaenia1
|
SRX4939852
|
SRR8113473
|
GSM3447567: Trinity_A. argotaenia1; Amentotaxus argotaenia; RNA-Seq
|
Transcriptomic analysis revealed the mechanisms involved in the differential accumulation of taxoids, flavonoids and hormones among three Taxaceae trees
|
|
|
|
|
RNA-Seq_SHS-Leaf
|
SRX3296043
|
SRR6187006
|
Transcriptome sequences of leaf tissue from Amentotaxus argotaenia
|
To assemble a transcriptome de novo and to accurately evaluate polymorphisms and enhance our understanding of evolutionary potentials of Amentotaxus argotaenia
|
A total of 56 A. argotaenia individuals were sampled from four of its natural populations. Fresh leaves were collected and desiccated. Genomic DNA was isolated using the modified cetyltrimethylammonium bromide method
|
||
|
Amentotaxus argotaenia
|
SRX3058226
|
SRR5892533
|
Gymnosperms transcriptome
|
Numerous attempts have been made to resolve phylogenetic relation-ships among the five seed plant lineages using morphological characters andmolecular data, but without consensus, especially as regards the relationship of the Gnetales. A high quality of sequence alignment was finallyused in the phylogenetic analysis, which strongly supportsGnetales as sister to Pinaceae (the Gnepine hypothesis). Wefound that significant incongruence among gene trees ismostly caused by partial convergent molecular evolution orhomoplasy between Gnetales and angiosperms.
|
New transcriptomic data were generated from 22 species repre-senting all 13 families of gymnosperms. Transcriptomic data ofthree fern species were downloaded from NCBI, and 11 filteredprotein-coding DNA and amino acid (AA) databases as well astwo contig datasets of angiosperms were retrieved from Phyto-zome and UGA, respectively. Young leaves or buds were collected and stored in RNAlatersolution (Life Technologies, CA, USA). Total RNAs were isolatedusing the RNAplant Plus Reagent (Tiangen, Beijing, China) anddigested by DNaseI(Promega, Madison, USA). For each species,approximately 5mg of total RNAs were used to construct thecDNA library
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IAJW
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ERX2099860
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ERR2040803
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Illumina HiSeq 2000 paired end sequencing
|
1KP is an international multidisciplinary consortium acquiring large-scale gene sequences for the Viridiplantae (green plants), incorporating at some phylogenetic/taxonomic level nearly all known species from angiosperms to algae. This study follows initial data releases with the remaining sequence data.
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Amentotaxus argotaenia replicate 1
|
SRX1787319
|
SRR3560667
|
GSM2171498: Amentotaxus argotaenia replicate 1; Amentotaxus argotaenia; Bisulfite-Seq
|
The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae the authors provide novel insights into the evolution of gbM and its underlying mechanism.
|
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. Libraries were prepared following the steps provided in Urich et al. (2015; Nature Protocols)
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Amentotaxus formosania replicate 1
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GSM2171499
|
SRR3560668
|
GSM2171499: Amentotaxus formosania replicate 1; Amentotaxus formosana; Bisulfite-Seq
|
The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae the authors provide novel insights into the evolution of gbM and its underlying mechanism.
|
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. Libraries were prepared following the steps provided in Urich et al. (2015; Nature Protocols)
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A_spicata
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ERX2099916
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ERR2040859
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ERX2099916: Illumina HiSeq 2000 paired end sequencing
|
The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae the authors provide novel insights into the evolution of gbM and its underlying mechanism.
|
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. Libraries were prepared following the steps provided in Urich et al. (2015; Nature Protocols)
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Cephalotaxus hainanensis
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SRX648273
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SRR1509462
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Cephalotaxus hainanensis Transcriptome or Gene expression
|
Cephalotaxus hainanensis, an endangered plant, is known to contain several metabolites with anti-cancer activity. Despite its clinical impact, the alkaloid metabolism of this species has remained largely uncharacterized. The potential of Cephalotaxus for metabolic engineering of medically interesting compounds has, so far, not been exploited, due to the almost complete lack of molecular information. The authors performed a high throughput RNA-seq analysis and assembled the transcriptome de novo. As proof of principle for medically interesting pathways, gene fragments related to paclitaxel biosynthesis were searched and detected. This finding demonstrates the potential of the annotated transcriptome as information resource for the biotechnological exploitation of plant secondary metabolism.
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Seedlings of C. hainanensis were collected in the greenhouse. The leaves were harvested from 2-year old plants and frozen immediately in liquid nitrogen. Total RNA was extracted using a CTAB-based isolation procedure [18], and purified with the Axyprep multisource total RNA miniprep kit.
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C_harringtonia Old Needles-1 transcriptome
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SRX5822350
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SRR9045792
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Cephalotaxus harringtonia fastigiata Gene Expression Profiling
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Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia Stem-5 transcriptome
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SRX5822349
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SRR9045793
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Cephalotaxus harringtonia fastigiata Gene Expression Profiling
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Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia New Needles-1 transcriptome
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SRX5822348
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SRR9045794
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Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia Stem-3 transcriptome
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SRX5822347
|
SRR9045795
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
|
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C_harringtonia Stem-4 transcriptome
|
SRX5822346
|
SRR9045796
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
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|
C_harringtonia Old Needles-6 transcriptome
|
SRX5822345
|
SRR9045797
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia Old Needles-5 transcriptome
|
SRX5822344
|
SRR9045798
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
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C_harringtonia Old Needles-2 transcriptome
|
SRX5822343
|
SRR9045799
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia Old Needles-4 transcriptome
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SRX5822342
|
SRR9045800
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia New Needles-5 transcriptome
|
SRX5822341
|
SRR9045801
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia Old Needles-3 transcriptome
|
SRX5822340
|
SRR9045802
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia Root-1 transcriptome
|
SRX5822339
|
SRR9045803
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia Stem-2 transcriptome
|
SRX5822338
|
SRR9045804
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
|
|
C_harringtonia Stem-1 transcriptome
|
SRX5822337
|
SRR9045805
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia New Needles-3 transcriptome
|
SRX5822336
|
SRR9045806
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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C_harringtonia New Needles-4 transcriptome
|
SRX5822335
|
SRR9045807
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
C_harringtonia Root-4 transcriptome
|
SRX5822334
|
SRR9045808
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
C_harringtonia New Needles-6 transcriptome
|
SRX5822333
|
SRR9045809
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
C_harringtonia Root-2 transcriptome
|
SRX5822332
|
SRR9045810
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
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|
C_harringtonia Root-3 transcriptome
|
SRX5822331
|
SRR9045811
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling
|
Cephalotaxus harringtonia fastigiata Gene Expression Profiling. Plant was fertilized with nutrient solution (Ionic Grow for Soil 3-1-5, Hydrodynamics International) and subsequently watered approximately once every two weeks. Growth conditions consisted of ambient laboratory temperature and lighting.
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|
|
|
C_harringtonia
|
ERX2099859
|
ERR2040802
|
Illumina HiSeq 2000 paired end sequencing
|
1000 Plant (1KP) Transcriptomes: The Remaining Data
|
|
|
|
|
C_harringtonia
|
ERX2099858
|
ERR2040801
|
Illumina HiSeq 2000 paired end sequencing
|
1000 Plant (1KP) Transcriptomes: The Remaining Data
|
|
|
|
|
C_harringtonia replicate 1
|
SRX1787342
|
SRR3560690
|
GSM2171521: Cephalotaxus harringtonia replicate 1; Cephalotaxus harringtonia; Bisulfite-Seq
|
The evolution of gene body methylation (gbM) and the underlying mechanism is poorly understood. By pairing the largest collection of CHROMOMETHYLTRANSFERASE (CMT) sequences (773) and methylomes (72) across land plants and green algae the authors provide novel insights into the evolution of gbM and its underlying mechanism.
|
DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. Libraries were prepared following the steps provided in Urich et al. (2015; Nature Protocols)
|
||
|
C_harringtonia
|
SRX025886
|
SRR064395
|
454 sequencing of Cephalotaxus harringtonia 'Prostrata' EST project
|
DOE Joint Genome Institute Cephalotaxus harringtonia ''Prostrata'' EST project
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C_oliveri
|
NC_021110.1
|
NC_021110.1
|
Cephalotaxus oliveri chloroplast, complete genome
|
The authors determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana.
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Total RNA was extracted following the protocol of RNAiso for Polysaccharide-rich Plant Tissue (Takara Bio Inc, Dalian, China). cDNA templates were synthesized using Reverse Transcriptase M-MLV Kit (Takara Bio Inc, Dalian, China).To examine whether the accD gene was transcribed, a reverse transcription (RT)-PCR was carried out using a pair of primers designed based on the full-length CDS of the gene in C. oliveri.
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