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草业学报 ›› 2014, Vol. 23 ›› Issue (6): 242-252.DOI: 10.11686/cyxb20140629

• 论文 • 上一篇    下一篇

基于高通量测序的海滨雀稗转录组学研究

贾新平,叶晓青,梁丽建,邓衍明,孙晓波,佘建明   

  1. 江苏省农业科学院农业生物技术研究所 江苏省农业生物学重点实验室,江苏 南京 210014
  • 收稿日期:2013-11-11 出版日期:2014-12-20 发布日期:2014-12-20
  • 作者简介:贾新平(1983-),男,山西晋城人,助理研究员,博士
  • 基金资助:
    江苏省盐土生物资源研究重点实验室开放课题(JKLBS2012003)资助

Transcriptome characteristics of Paspalum vaginatum analyzed with Illumina sequencing technology

JIA Xin-ping,YE Xiao-qing,LIANG Li-jian,DENG Yan-ming,SUN Xiao-bo,SHE Jian-ming   

  1. Provincial Key Laboratory of Agrobiology, Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
  • Received:2013-11-11 Online:2014-12-20 Published:2014-12-20

摘要: 采用新一代高通量测序技术Illumina HiSeq 2000对海滨雀稗叶片转录组进行测序,结合生物信息学方法开展基因表达谱研究和功能基因预测。通过测序,获得了47520544个序列读取片段(reads),包含了4752054400个碱基序列(bp)信息。对reads进行序列组装,获得81220个单基因簇(unigene),平均长度1077 bp,序列信息达到了87542503 bp。另外从长度分布、GC含量、表达水平等方面对unigene进行评估,数据显示测序质量好,可信度高。数据库中的序列同源性比较表明,46169个unigene与其他生物的已知基因具有不同程度的同源性。海滨雀稗转录组中的unigene根据GO功能大致可分为细胞组分、分子功能和生物学过程三大类48个分支,其中有大量unigene与代谢进程、结合活性和细胞进程相关。将unigene与COG数据库进行比对,根据其功能大致可分为25类。KEGG 数据库作为参考,依据代谢途径可将unigene定位到112个代谢途径分支,包括苯丙氨酸代谢通路、植物与病原物互作、植物激素生物合成和信号转导、黄酮类化合物合成、萜类骨架生物合成、脂类代谢、RNA降解等。SSR位点查找发现,从81220个unigene中共找到22721个SSR位点。SSR不同重复基序类型中,出现频率最高的为A/T,其次是CCG/CGG和AGC/CTG。本研究首次对海滨雀稗转录组进行了分析,为草坪草的分子生物学研究提供了宝贵的基因组数据来源。

Abstract: The transcriptome of Paspalum vaginatum leaf was sequenced using an Illumina HiSeq 2000 platform, which is a new generation of high-throughput sequencing technology used to study expression profiles and to predict functional genes. In the target sample, a total of 47520544 reads containing 4752054400 bp of sequence information were generated. A total of 81220 unigenes containing 87542503 bp sequence information were formed by initial sequence splicing, with an average read length of 1077 bp. Unigene qualities for several aspects were assessed, such as length distribution, GC content and gene expression level. The sequencing data was of high quality and reliability. The 46169 unigenes were annotated using BLAST searches against the Nr, Nt and SwissProt databases. All the assembled unigenes could be broadly divided into biological processes, cellular components and 48 branches of molecular function categories by gene ontology, including metabolic process, binding and cellular processes. The unigenes were further annotated based on COG category, which could be grouped into 25 functional categories. The unigenes could be broadly divided into 112 classes according to their metabolic pathway, including the phenylalanine metabolism pathway, plant-pathogen interaction, plant hormone biosynthesis and signal transduction, flavonoid biosynthesis, terpenoid backbone biosynthesis, lipid metabolism, and RNA degradation. There were 22721 SSR in 81220 unigenes and in the SSR, A/T was the highest repeat, following by CCG/CGG and AGC/CTG. This study is the first comprehensive transcriptome analysis for Paspalum vaginatum, providing valuable genome data sources for the molecular biology of this grass.

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