Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato
Accumulation, functional annotation, and comparative analysis of expressed sequence tags in eggplant (Solanum melongena L.), the third pole of the genus Solanum species after tomato and potato
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DOI：
10.1016/j.gene.2009.10.006
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发表时间：
2010-01-15
期刊：
影响因子：
3.5
通讯作者：
Ohyama, Akio
中科院分区：
文献类型：
--
作者：
Fukuoka, Hiroyuki;Yamaguchi, Hirotaka;Ohyama, Akio
茄子（Solanum melongena L）是一种广泛种植的茄属蔬菜作物，其由1000多个物种组成，具有广泛的遗传和表型变异。与番茄和马铃薯不同，茄属作物属于马铃薯亚属，并已成为全面基因组研究的目标，茄子是旧大陆特有的，属于不同的亚属，Leptostemonum，因此，将是茄属比较分子生物学的独特成员。在这项研究中，超过60，000个来自不同组织和处理的茄子cDNA克隆从5 '-和3'-末端进行测序，并构建了由16，245个独特序列组成的单基因集。功能注释的基础上的序列相似性已知的植物参考数据集显示的功能类别的分布几乎类似于番茄，而1316 unigenes被认为是茄子特异性。基于序列的比较分析表明，茄子及其野生种Solanum torvum与马铃薯亚属植物聚为一类，而所有茄属植物与辣椒属植物聚为一类。微卫星基序的分布在不同物种间存在差异，可能与系统发育关系相一致。此外，茄子unigene数据集表现出其效用的转录组分析的SAGE策略，其中相当数量的短标签序列的兴趣被成功地分配到unigene及其功能注释。本研究中开发的茄子ESTs和16 k unigene集不仅为茄子本身的分子遗传学和育种提供了有用的资源，而且还为扩大茄属物种的比较生物学范围提供了有用的资源。(C)2009 Elsevier B. V.保留所有权利。
Eggplant (Solanum melongena L) is a widely grown vegetable crop that belongs to the genus Solanum, which is comprised of more than 1000 species of wide genetic and phenotypic variation. Unlike tomato and potato, Solanum crops that belong to subgenus Potatoe and have been targets for comprehensive genomic studies, eggplant is endemic to the Old World and belongs to a different subgenus, Leptostemonum, and therefore, would be a unique member for comparative molecular biology in Solanum. In this study, more than 60,000 eggplant cDNA clones from various tissues and treatments were sequenced from both the 5'- and 3'-ends, and a unigene set consisting of 16,245 unique sequences was constructed. Functional annotations based on sequence similarity to known plant reference datasets revealed a distribution of functional categories almost similar to that of tomato, while 1316 unigenes were suggested to be eggplant-specific. Sequence-based comparative analysis using putative orthologous gene groups setup by reciprocal sequence comparison among six solanaceous species suggested that eggplant and its wild ally Solanum torvum were clustered separately from subgenus Potatoe species, and then, all Solanum species were clustered separately from the genus Capsicum. Microsatellite motif distribution was different among species and likely to be coincident with the phylogenetic relationships. Furthermore, the eggplant unigene dataset exhibited its utility in transcriptome analysis by the SAGE strategy where a considerable number of short tag sequences of interest were successfully assigned to unigenes and their functional annotations. The eggplant ESTs and 16k unigene set developed in this study would be a useful resource not only for molecular genetics and breeding in eggplant itself, but for expanding the scope of comparative biology in Solanum species. (C) 2009 Elsevier B.V. All rights reserved.