Góngora-Castillo Elsa, Fajardo-Jaime Rubén, Fernández-Cortes Araceli, Jofre-Garfias Alba E, Lozoya-Gloria Edmundo, Martínez Octavio, Ochoa-Alejo Neftalí, Rivera-Bustamante Rafael
Bioinformation. 2012;8(1):43-7. doi: 10.6026/97320630008043. Epub 2012 Jan 6.
Chili pepper (Capsicum annuum) is an economically important crop with no available public genome sequence. We describe a genomic resource to facilitate Capsicum annuum research. A collection of Expressed Sequence Tags (ESTs) derived from five C. annuum organs (root, stem, leaf, flower and fruit) were sequenced using the Sanger method and multiple leaf transcriptomes were deeply sampled using with GS-pyrosequencing. A hybrid assembly of 1,324,516 raw reads yielded 32,314 high quality contigs as validated by coverage and identity analysis with existing pepper sequences. Overall, 75.5% of the contigs had significant sequence similarity to entries in nucleic acid and protein databases; 23% of the sequences have not been previously reported for C. annuum and expand sequence resources for this species. A MySQL database and a user-friendly Web interface were constructed with search-tools that permit queries of the ESTs including sequence, functional annotation, Gene Ontology classification, metabolic pathways, and assembly information. The Capsicum Transcriptome DB is free available from http://www.bioingenios.ira.cinvestav.mx:81/Joomla/
辣椒（Capsicum annuum）是一种具有重要经济价值的作物，但目前尚无公开的基因组序列。我们描述了一种有助于辣椒研究的基因组资源。利用桑格测序法对来自辣椒五个器官（根、茎、叶、花和果实）的表达序列标签（EST）文库进行了测序，并利用GS-焦磷酸测序法对多个叶片转录组进行了深度采样。通过对1,324,516条原始读数进行混合组装，得到了32,314个高质量重叠群，通过与现有辣椒序列的覆盖度和一致性分析进行了验证。总体而言，75.5%的重叠群与核酸和蛋白质数据库中的条目具有显著的序列相似性；23%的序列此前未在辣椒中报道过，从而扩展了该物种的序列资源。构建了一个MySQL数据库和一个用户友好的网络界面，带有搜索工具，可用于查询EST，包括序列、功能注释、基因本体分类、代谢途径和组装信息。辣椒转录组数据库可从http://www.bioingenios.ira.cinvestav.mx:81/Joomla/免费获取。
