Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish
Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish
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DOI：
10.1007/s00299-012-1259-3
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发表时间：
2012-08-01
影响因子：
6.2
通讯作者：
Wang, Fengde
中科院分区：
文献类型：
--
作者：
Wang, Shufen;Wang, Xiufeng;Wang, Fengde
萝卜块根是一种重要的蔬菜，但目前还没有足够的转录和基因组数据来了解块根形成和发育的分子机制。高通量转录测序是为基因发现和分子标记开发生成大量转录序列数据集所必需的。在这项研究中，使用Illumina配对末端测序技术总共产生了1.073亿个干净的读数。从头组装产生61,554个单基因，平均长度为820个碱基对。根据与已知蛋白质或核苷酸的序列相似性搜索，85.51%(52,634)、90.18%(55,507)和54%(33,242)的共有序列分别与Nr、NT和Swiss-Prot数据库中的序列同源性。其中21,109个和17,343个非基因分别被归入基因本体论类别和同源类群。在京都基因和基因组数据库中，共有27,809个非基因被分配到123条途径中。对幼苗发育早期和后期文库的转录差异分析表明，淀粉和蔗糖代谢以及苯丙烷类化合物的生物合成可能是块茎形成过程中的主要代谢事件，植物激素可能在这一发育过程中起关键作用。共鉴定出14,641个潜在的EST-SSR，共扩增出12,733对2,511对SSR。综上所述，本研究为我们了解萝卜块根的形成和发育提供了线索，也为萝卜新基因的发现和分子标记辅助选择育种提供了有价值的序列资源。
The tuberous root of radish is an important vegetable, but insufficient transcriptomic and genomic data are currently available to understand the molecular mechanisms underlying tuberous root formation and development. High-throughput transcriptomic sequencing is essential to generate a large transcript sequence data set for gene discovery and molecular marker development. In this study, a total of 107.3 million clean reads were generated using Illumina paired-end sequencing technology. De novo assembly generated 61,554 unigenes with an average length of 820 bp. Based on a sequence similarity search with known proteins or nucleotides, 85.51 % (52,634), 90.18 % (55,507) and 54 % (33,242) consensus sequences showed homology with sequences in the Nr, Nt and Swiss-Prot databases, respectively. Of these annotated unigenes, 21,109 and 17,343 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. A total of 27,809 unigenes were assigned to 123 pathways in the Kyoto Encyclopedia of Genes and Genomes database. Analysis of transcript differences between libraries from the early and late seedling developmental stages demonstrated that starch and sucrose metabolism and phenylpropanoid biosynthesis may be the dominant metabolic events during tuberous root formation and plant hormones probably play critical roles in regulation of this developmental process. In total, 14,641 potential EST-SSRs were identified among the unigenes, and 12,733 primer pairs for 2,511 SSR were obtained. Summarily, this study gave us a clue to understand the radish tuberous root formation and development, and also provided us with a valuable sequence resource for novel gene discovery and marker-assisted selective breeding in radish.De novo assembled and characterized the radish tuberous root transcriptome; explored the mechanism of radish tuberous root formation; development of EST-SSR markers in radish.