基于RNA-Seq技术的甘蔗参考转录组建立及分析  

Establishment and Analysis on Reference Transcriptome of Sugarcane Based on RNA-Seq Technology

作　　者：李穆[1] 程志远[1] 石莹[1] 何平[1] 王先宏[1] 何丽莲[1] 李富生[1] 

机构地区：[1]云南农业大学甘蔗研究所,昆明650201

出　　处：《分子植物育种》2015年第2期355-360,共6页Molecular Plant Breeding

基　　金：云南省现代农业甘蔗产业技术体系建设项目(2009-2014);云南省重点新产品开发计划项目(2012BB014);云南省高原山地作物可持续生产系统研究创新团队项目(云科人发[2012]18号)共同资助

摘　　要：本研究基于RNA-Seq技术建立了一个由3个甘蔗原始亲本和8个不同来源的甘蔗栽培品种/系构成的甘蔗参考转录组,并进行生物信息学相关分析。研究结果表明:对供试材料+1叶RNA混合样本进行转录组测序,可组装出98 945条Contig,从中找到5 806个SSR位点,其中三核苷酸重复最多、六核苷酸重复最少,CCG/CGG出现的频率最高。进一步处理Contig获得75 656条Unigene,将所有的Unigene与Nr数据库、Swiss-Prot数据库、KEGG数据库和COG数据库进行Blast,有53 951条Unigene得到注释。在Nr和KEGG注释结果基础上,对Unigene进行GO和KEGG功能分类,分别获得44个功能小组和123个Pathway注释。研究结果可为研究甘蔗在不同时空条件下的差异基因表达奠定基础。This research established a reference transcriptome of sugarcane which consists of three sugarcane parents and eight sugarcane cultivars/lines from different sources based on RNA-Seq technology.By related bioinformatics analysis,the results showed that 98 945 contigs were obtained through sequencing the mixed samples of sugarcane ＋1 leaf by transcriptome sequencing.There are 5 806 SSR loci were found in 98 945 contigs.The characteristic of SSR distribution showed that tri-nucleotide repeat was the highest,and the lowest was hexanucleotide repeat.The types of SSR were analyzed that CCG/CGG was the highest repeat.By further processing of contigs,75 656 unigenes were obtained,for which 53 951 unigenes had been annotated through blasting with Nr database,Swiss-Prot database,KEGG database and the COG database.Base on results of Nr and KEGG annotation,44 functional groups and 123 pathways were obtained through GO and KEGG functional classification.These results laid the foundation for studying the gene＇s expression of sugarcane at spatial and temporal difference.

关 键 词：甘蔗 RNA-SEQ 参考转录组 UNIGENE SSR 

分 类 号：S566.1[农业科学—作物学]