Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68
Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68
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DOI：
10.1007/s11033-011-1102-x
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发表时间：
2012-03-01
影响因子：
2.8
通讯作者：
Park, Yong-Jin
中科院分区：
文献类型：
--
作者：
Lu, Fu-Hao;Cho, Myeong-Cheoul;Park, Yong-Jin
高通量合成测序的转录组是分子标记的良好资源。在本研究中，我们展示了使用 454 GS-FLX 焦磷酸测序分析红辣椒 (Capsicum annuum L. TF68) 转录组的大规模并行合成测序的实用性。通过生成平均长度为 375 碱基对 (bp) 的约 30.63 兆碱基 (Mb) 的表达序列标签 (EST) 数据，通过原始读段组装获得了 9,818 个重叠群和 23,712 个单例。使用针对 NCBI 非冗余和 UniProt 蛋白质数据库的 BLAST 比对，30% 的暂定共有序列被分配给特定功能注释，而 24% 返回未知功能的比对，剩下高达 46% 没有比对。使用 FunCat 进行功能分类显示，具有假定已知功能的序列分布在 18 个类别中。通过与番茄（Solanum lycopersicum）假分子比对，所有unigenes在染色体上的分布大致相等。此外，以布康成熟果实cDNA集合（dbEST ID：23667）为参考，发现了1,536个高质量的单核苷酸差异。此外，从 614 个重叠群中挖掘了 758 个简单序列重复 (SSR) 基序位点，并从中设计了 572 个引物组。 SSR 基序对应于二核苷酸基序和三核苷酸基序（分别为 27.03% 和 61.92%）。这些分子标记在连锁作图和关联作图研究中可能具有重要的应用价值。
Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.