Hevea brasiliensis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA319415 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3423350_1.fastq.gz | Fastqsanger.gz | |||
| SRR3423350_2.fastq.gz | Fastqsanger.gz | |||
| SRR3423347_1.fastq.gz | Fastqsanger.gz | |||
| SRR3423347_2.fastq.gz | Fastqsanger.gz | |||
| SRR3423348_1.fastq.gz | Fastqsanger.gz |
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Project description:We report transcriptome data of four kinds of bark samples from the Hevea brasiliensis clone CATAS7-33-97 by use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly. The output of sequenced data showed that a total of 323,842,182 clean reads with average length of 90 nt were generated in four samples. Totally 67,873 uingenes with an average length of 750 nt and a N50 of 1,222 nt were assembled through transcriptome de novo assembly. The all assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. The comparative analysis of the transcriptome data performed with the criteria of FDR ≤ 0.001 and |log2 Ratio| ≥ 1. As a result, 15,780 different expression unigenes (8,646 up and 7,134 down ) were detected in early libraries (Control-A versus COR-A) upon coronatine treatment, and 19,824 different expression unigenes (7,711 up and 12,113 down) were detected in late libraries (Control-B versus COR-B) upon coronatine treatment. Functional analysis of different expression unigenes showed that mass of unigenes were annotated in multiple signaling pathways. Comparative transcriptome analysis of inner bark in response to coronatine reveals a new insight into the signal networks for the secondary laticifer differentiation from vascular cambia in rubber tree.
2017-02-14 | GSE80596 | GEO
Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information. The transcriptome of latex and leaf in Hevea brasiliensis
2011-09-01 | E-GEOD-26514 | biostudies-arrayexpress
Project description:We report here the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of two Hevea brasiliensis clones (RY8-79 and PR107). The output of sequenced data showed that more than 26 million sequence reads with average length of 90nt were generated in both clones. Totally 51829 unigenes (mean size = 640 bp) were assembled through transcriptome de novo assembly, which represent more than 16-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Base on limit rule with FDR≤0.001 and |log2 Ratio|≥1, 6726 different expression unigenes (3018 up and 3708 down) were detected as PR107 versus RY8-79. Functional analysis showed mass of categories were reprogrammed between two clones, which relate latex generation and expelling difference between them. As a comparative transcriptome analysis, the results obtained here will greatly expand our understanding of physiological differences among varieties in molecular level and will contribute t The transcriptome of latex in Hevea brasiliensis
2015-03-29 | E-GEOD-59981 | biostudies-arrayexpress
Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information.
2011-09-01 | GSE26514 | GEO
Project description:We report here the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of two Hevea brasiliensis clones (RY8-79 and PR107). The output of sequenced data showed that more than 26 million sequence reads with average length of 90nt were generated in both clones. Totally 51829 unigenes (mean size = 640 bp) were assembled through transcriptome de novo assembly, which represent more than 16-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Base on limit rule with FDR≤0.001 and |log2 Ratio|≥1, 6726 different expression unigenes (3018 up and 3708 down) were detected as PR107 versus RY8-79. Functional analysis showed mass of categories were reprogrammed between two clones, which relate latex generation and expelling difference between them. As a comparative transcriptome analysis, the results obtained here will greatly expand our understanding of physiological differences among varieties in molecular level and will contribute t
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Project description:Hevea brasiliensis subsp. brasiliensis Transcriptome or Gene expression
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