Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
Plant Cell Rep. 2012 Aug;31(8):1437-47. doi: 10.1007/s00299-012-1259-3. Epub 2012 Apr 4.
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.
萝卜的块根是一种重要的蔬菜，但目前缺乏转录组和基因组数据来了解块根形成和发育的分子机制。高通量转录组测序对于生成用于基因发现和分子标记开发的大型转录序列数据集至关重要。在这项研究中，使用 Illumina 配对末端测序技术共生成了 1.073 亿个清洁读取。从头组装生成了 61554 个平均长度为 820bp 的 unigenes。基于与已知蛋白质或核苷酸的序列相似性搜索，分别有 85.51%（52634 个）、90.18%（55507 个）和 54%（33242 个）的一致性序列与 Nr、Nt 和 Swiss-Prot 数据库中的序列同源。在这些注释的 unigenes中，分别有 21109 个和 17343 个 unigenes被分配到基因本体类别和直系同源簇中。共有 27809 个 unigenes被分配到京都基因与基因组百科全书数据库中的 123 条途径。文库之间的转录差异分析早期和晚期幼苗发育阶段表明，淀粉和蔗糖代谢和苯丙烷生物合成可能是块根形成和植物激素发育过程中的主要代谢事件，可能在调节这个发育过程中发挥关键作用。总共在 unigenes 中鉴定出 14641 个潜在的 EST-SSR，获得了 12733 对 2511 个 SSR 的引物。总之，这项研究为我们理解萝卜块根的形成和发育提供了线索，也为萝卜中新基因的发现和标记辅助选择育种提供了宝贵的序列资源。
从头组装和表征萝卜块根转录组；探讨萝卜块根形成和发育的机制；萝卜 EST-SSR 标记的开发。
