RNA-Seq analysis for transcriptome assembly, gene identification, and SSR mining in ginkgo (Ginkgo biloba L.)
RNA-Seq analysis for transcriptome assembly, gene identification, and SSR mining in ginkgo (Ginkgo biloba L.)
复制标题
用于银杏 (Ginkgo biloba L.) 转录组组装、基因鉴定和 SSR 挖掘的 RNA-Seq 分析
DOI：
10.1007/s11295-015-0868-8
复制
发表时间：
2015-06-01
影响因子：
2.4
通讯作者：
Shi, Huazhong
中科院分区：
文献类型：
--
作者：
Han, Shiming;Wu, Zhenjiang;Shi, Huazhong
银杏（Ginkgo biloba L.）在植物界分类独特，作为药用植物有着悠久的历史，是一种独特的树种，但对银杏的遗传信息和分子过程却知之甚少。本研究利用Trinity对银杏无菌苗长度为75 bp的6368万个对端reads进行了组装，得到70752个转录本和49396个唯一转录本。在39,941个具有编码区的唯一转录本中，有24,645个唯一转录本在公共数据库中至少有一次命中。仅有15,154个独特的转录本被注释到52个基因本体（GO）功能类别中。分析了50个和43个序列，分别与黄酮类化合物和银杏内酯/双叶内酯的合成有关，揭示了催化代谢途径各步骤的推定酶。序列分析鉴定出一个银杏查尔酮异构酶基因（GbCHI1），该基因编码黄酮类生物合成途径的关键酶之一，其蛋白质序列与先前鉴定的GbCHI基因不同。系统发育分析表明，GbCHI1与云杉的GbCHI和查尔酮异构酶接近，其表达水平与不同组织中黄酮类化合物的含量一致。在转录库中发现4000个简单重复序列（SSRs），设计了1513条SSR位点的引物。
Ginkgo (Ginkgo biloba L.) is a unique tree due to its distinctive classification in the plant kingdom and a long history as a medicinal plant, yet the genetic information and molecular processes in ginkgo have been largely lacking. In this study, 63.68 million paired-end reads from the asepsis seedling of ginkgo with lengths of 75 bp were assembled using Trinity, and 70,752 transcripts and 49,396 unique transcripts were generated. Among the 39,941 unique transcripts with coding regions, 24,645 unique transcripts had at least one hit in the public databases. And only 15,154 unique transcripts were annotated into 52 gene ontology (GO) functional categories. There were 50 and 43 sequences analyzed to be involved in the synthesis of flavonoids and ginkgolide/bilobalide, respectively, uncovering the putative enzymes catalyzing each step of the metabolic pathways. Sequence analysis identified a ginkgo chalcone isomerase gene (GbCHI1) encoding one of the key enzymes in the flavonoid biosynthesis pathway and exhibiting differences on protein sequences from the previously identified GbCHI. Phylogenetic analysis showed that GbCHI1 is close to GbCHI and the chalcone isomerase from Picea sitchensis, and the expression levels of GbCHI1 are coincided with the contents of flavonoids in different tissues. Furthermore, 4000 simple sequence repeats (SSRs) were found in the transcript library, and 1513 PCR primers of the SSR loci were designed.