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SRA of transcriptome of Hevea brasiliensis

ABSTRACT: 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'.

ORGANISM(S): Hevea brasiliensis

PROVIDER: GSE67559 | GEO | 2018/03/25

REPOSITORIES: GEO

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Project description:Gastrodia elata Blume (Orchidaceae) is an important Chinese medicine with several functional components. In the life cycle of G. elata, the orchid develops a symbiotic relationship with two compatible mycorrhizal fungi Mycena spp. and Armillaria mellea during seed germination to form vegetative propagation corm and vegetative growth to develop tubers, respectively. Gastrodin (p-hydroxymethylphenol-beta-D-glucoside) is the most important functional component in G. elata, and gastrodin significantly increases from vegetative propagation corms to tubers. To address the gene regulation mechanism in gastrodin biosynthesis in G. elata, a comparative analysis of de novo transcriptome sequencing among the vegetative propagation corms and tubers of G. elata and A. mellea was conducted using deep sequencing. Transcriptome comparison between the vegetative propagation corms and juvenile tubers of G. elata revealed 582 differentially expressed unigenes, of which 415 and 167 genes were, respectively up-regulated (fold-change â?¥ 2, p-value < 0.05) and down-regulated (fold-change â?¤ 0.5, p-value <0.05) in juvenile tubers. After Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, forty-seven up-regulated unigenes with enzyme commission (EC) were assigned to 269 isogroups involved in 100 different pathways, and twenty-four down-regulated unigenes with enzyme commission (EC) were assigned to 586 isogroups, involved in 167 different pathways. The analysis of the isogroup genes from all pathways revealed that the two unigenes at locus 25,051 (one of monooxygenases) and locus 22,288 (one of glycosyltransferases) might participate in hydroxylation and glucosylation in the gastrodin biosynthetic pathway. The gene expression of the two unique unigenes encoding monooxygenase and glycosyltransferase significantly increases from vegetative propagation corms to tubers, and the molecular basis of gastrodin biosynthesis in the tubers of G. elata is proposed. Transcriptome comparative between vegetative propagation corms and tubers of G. elata, and between tubers of G. elata (symbiosis A. mellea) and A. mellea

Project description:Gastrodia elata Blume (Orchidaceae) is an important Chinese medicine with several functional components. In the life cycle of G. elata, the orchid develops a symbiotic relationship with two compatible mycorrhizal fungi Mycena spp. and Armillaria mellea during seed germination to form vegetative propagation corm and vegetative growth to develop tubers, respectively. Gastrodin (p-hydroxymethylphenol-beta-D-glucoside) is the most important functional component in G. elata, and gastrodin significantly increases from vegetative propagation corms to tubers. To address the gene regulation mechanism in gastrodin biosynthesis in G. elata, a comparative analysis of de novo transcriptome sequencing among the vegetative propagation corms and tubers of G. elata and A. mellea was conducted using deep sequencing. Transcriptome comparison between the vegetative propagation corms and juvenile tubers of G. elata revealed 582 differentially expressed unigenes, of which 415 and 167 genes were, respectively up-regulated (fold-change ≥ 2, p-value < 0.05) and down-regulated (fold-change ≤ 0.5, p-value <0.05) in juvenile tubers. After Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, forty-seven up-regulated unigenes with enzyme commission (EC) were assigned to 269 isogroups involved in 100 different pathways, and twenty-four down-regulated unigenes with enzyme commission (EC) were assigned to 586 isogroups, involved in 167 different pathways. The analysis of the isogroup genes from all pathways revealed that the two unigenes at locus 25,051 (one of monooxygenases) and locus 22,288 (one of glycosyltransferases) might participate in hydroxylation and glucosylation in the gastrodin biosynthetic pathway. The gene expression of the two unique unigenes encoding monooxygenase and glycosyltransferase significantly increases from vegetative propagation corms to tubers, and the molecular basis of gastrodin biosynthesis in the tubers of G. elata is proposed.

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SRA of transcriptome of Hevea brasiliensis

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