参薯microRNA基因挖掘与特征分析

Identification and Characterization of microRNA Genes in Dioscorea alata

参薯(Dioscorea alata),其地下块茎富含淀粉、多糖、蛋白质等多种营养物质,是热带和亚热带地区重要的主食之一,同时也是药物和生物质能源的原料。由于可获得的序列非常有限,参薯分子水平研究非常薄弱。在本研究中,我们以现有的参薯基因组序列和表达序列为基础,使用生物信息学的方法,挖掘参薯序列中的microRNA基因,并对这些基因的表达特征进行分析。根据miRBase数据库中公布的成熟miRNA序列和参薯基因组,预测属于参薯miR159、miR164、miR167和miR168家族的miRNA基因13个。于此同时,我们根据参薯的表达序列,预测了这些家族的靶基因共17个,并对靶基因进行了功能注释。之后,我们使用RT-PCR检测13个miRNA在参薯叶片、缠绕茎、块茎等多个组织的表达,找到了5个miRNA基因在块茎中表达,有可能块茎发育相关。本研究为进一步探索miRNA在参薯块茎发育中的功能,为构建miRNA调控块茎发育网络提供信息,为改良参薯薯型提供帮助。

Water yam(Dioscorea alata), whose tubers are rich in starch, polyose, and proteins, is an important staple in tropical and subtropical regions and used as raw material for medicine and biomass energy. Because of the limitation of available sequence information, the researches about water yam on molecular level are still weak.In this study, we used bioinformatics methods to identify microRNA genes based on available genomic and expressed sequences of water yam, and then further verify their expression patterns. A total of 13 miRNA for four miRNA families-miR159, miR164, miR167 and miR168-were identified based mature miRNA sequences released in the miRBase database and published genomic sequence of water yam. Moreover, 17 targeted genes for these miRNA genes were predicted and annotated. RT-PCR was performed to verify the expression of these miRNA in different tissues of Dioscorea alata, and five key miRNA genes were selected as candidates related to tuber development. This study provides a foundation for exploring the functions of miRNA in tuber development and supplying information for gene network around miRNA, and lays a theoretical foundation for the shape improvement of water yam.