Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis.
Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis.
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DOI：
10.1093/dnares/dsw056
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发表时间：
2017-04-01
期刊：
影响因子：
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通讯作者：
Matsui M
中科院分区：
文献类型：
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作者：
Makita Y;Ng KK;Veera Singham G;Kawashima M;Hirakawa H;Sato S;Othman AS;Matsui M
天然橡胶具有其他乳胶生产厂的产品或石油化学生产的合成橡胶无法替代的独特物理性能。来自巴西橡胶树的橡胶是这种具有顺式聚异戊二烯结构的天然橡胶的主要商业来源。为了可持续地生产足够的橡胶以满足需求，阐明乳胶生产中的分子机制是至关重要的。为此，我们首先构建了RRIM 600品种的橡胶全长cDNA文库，并通过Sanger法和Illumina测序仪分别对大约20000个克隆和15000多个contigs进行了测序。利用这些数据，我们更新了大约5500个基因结构，并新注释了大约9500个转录起始位点。其次，为了阐明橡胶的生物合成途径及其转录调控，我们进行了组织特异性和品种特异性RNA-Seq分析。利用我们最近发表的基因组序列，我们确认了橡胶生物合成基因的表达模式。我们的数据表明，细胞质甲基戊酸（MVA）途径是乳胶生产中类异戊二烯生物合成的主要途径。除了已被充分研究的聚合因子外，我们认为橡胶延伸因子8 （REF8）是顺式聚异戊二烯生物合成的候选因子。我们还确定了39个转录因子可能是乳胶生产的关键调节因子。通过RNA-Seq方法对另外两个品种RRIM 901和pb350的表达谱进行分析，揭示了高产品种和抗病品种之间可能存在的表达差异。
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar.