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| Status |
Public on Mar 25, 2018 |
| Title |
SRA of transcriptome of Hevea brasiliensis |
| Organism |
Hevea brasiliensis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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 (93-114 and Reken501). Illumina sequencing generated a total of about 7-8G raw reads from each of the six batches (two batches for control and four batches for cold-treatment) of rubber tree clone 'Reken501' and '93-114', respectively. By using these reads, 167,911 unigenes with an average length of 847 bp were obtained by de novo assembly with a series of optimized parameters. Base on limit rule with FDR≤0.001 and |log2 Ratio|≥1, 2052 unigenes were up-regulated and 3440 unigenes were down-regulated under 1 h cold treatment in 'Reken501', whereas 2403 unigenes were up-regulated and 18376 unigenes were down-regulated under 1 h cold treatment in'93-114', and the amounts of up-regulated and down-regulated unigenes were respectively 6923 and 6282 in 'Reken501', whereas it was respectively 5295 unigenes and 21229 unigenes in'93-114' . Functional analysis showed mass of categories were reprogrammed between two clones. In detail,anthocyanin, flavonoid, isoflavonoid biosynthesis and starch and sucrose metabolism were shown more active in the cold-sensitive clone 'Reken 501', while the nitrogen metabolism, vitamin B6 metabolism, biosynthesis of unsaturated fatty acids and other processes of circadian rhythm-plant, spliceosome and RNA polymerase were more robust in the relatively cold-tolerant clone '93-114'. Moreover, the 'heat' module and 'Thinredoxin' module in the cellular stress response were highly induced in clone '93-114'.
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| Overall design |
The transcriptome of leaf (control and cold treatment of Reken501 and 93-114) in Hevea brasiliensis
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| Contributor(s) |
Deng X, Wang J, Tian W |
| Citation(s) |
29563566 |
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| Submission date |
Apr 03, 2015 |
| Last update date |
May 22, 2019 |
| Contact name |
Wei-Min Tian |
| Organization name |
Rubber Research Institute
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| Department |
Chinese Academy of Tropical Agricultural Sciences
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| Street address |
Baodao Village
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| City |
Danzhou |
| State/province |
Hainan |
| ZIP/Postal code |
571737 |
| Country |
China |
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| Platforms (1) |
| GPL11409 |
Illumina HiSeq 2000 (Hevea brasiliensis) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA280256 |
| SRA |
SRP056852 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67559_A0-vs-A1_diff.txt.gz |
4.4 Mb |
(ftp)(http) |
TXT |
| GSE67559_A0-vs-A2_diff.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
| GSE67559_All-Unigene.fa.gz |
33.6 Mb |
(ftp)(http) |
FA |
| GSE67559_B0-vs-B1_diff.txt.gz |
4.4 Mb |
(ftp)(http) |
TXT |
| GSE67559_B0-vs-B2_diff.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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