油莎豆转录组测序及生物信息学分析

Transcriptome Sequencing and Bioinformatic Analysis of Cyperus esculentus

为获得油莎豆的基因数据和初步了解其基因功能,本研究基于RNA-Seq技术对油莎豆幼苗叶片和根的混合样品进行转录组测序和生物信息学相关分析。对测序数据进行序列组装共获得19 607条Unigene,总长度为21 274 744 bp。将获得Unigene分别与COG、GO、KEGG、KOG、Pfam、Swissprot和Nr数据库进行比对,共计12 896条Unigene被注释,占总数的65.77%。其中7 527条Unigene在GO数据库中比对获得注释,根据功能分为细胞组分、分子功能和生物进程3大类52个亚类;12 288条Unigene在Nr数据库中获得注释,注释的同源序列主要来自菠萝;通过KOG数据库比对,7 271条Unigene被注释到25个类别中,其中参与一般功能、翻译后修饰及信号传导的注释基因最多。在所有Unigene中共检索到154 456个SNP位点,以碱基转换类型为主。本研究为油莎豆功能基因挖掘和分子标记开发提供理论基础。

In order t o obtain the gene data of Cyperus esculentus and preliminarily understand gene function, a mixture of seedling leaves and roots was used to establish a reference transcriptome sequencing and bioinformatic analysis of C. esculentus by RNA-Seq technology. 19 607 Unigenes with total length of 21 274 744 bp were generated after sequence assembly. 12 896 Unigenes were annotated in COG, GO, KEGG, KOG, Pfam, Swissprot and Nr public databases, accounting for 65.77% of the total. 7 527 Unigenes were annotated in GO database and were divided into cellular component, molecular function, and biological progress with 52 subgroups. 12 288 Unigenes were annotated in Nr database, and the annotated homologous sequences were mainly from Ananas comosus. There were 7 271 Unigenes annotated in 25 KOG function categories, the most annotated genes were involved in general function prediction, posttranslational modification and signal transduction. 154 456 SNPs were detected in all Unigenes, and the transition mutations are prevalent in those identified SNPs. This study provides a theoretical basis for the identification of functional genes and the development of molecular markers in C. esculentus.