基于高通量测序的野生毛葡萄转录组数据分析

Transcriptome Analysis of Vitis quinquangularis Rehd through High-throughput Sequencing

利用RNA-seq技术对所构建的野生毛葡萄(Vitis quinquangularis Rehd)叶片的转录组进行测定,对原始reads进行过滤和组装,得到了35 238条质量较高的unigene,平均长度为1 081 nt,N50为1 735 nt。基于NCBI蛋白质数据库(Nr)、蛋白质序列数据库(Swiss-Prot)、京都基因与基因组百科全书(KEGG)数据库和直系同源基因簇(COG)进行相似性比对,共注释了26 751条unigene,另有8 487条unigene未被注释。物种同源性显示与葡萄的同源性最高为74.48%。利用COG数据库将unigene分成25类,通过GO分类和KEGG富集性分析,将unigene分别归类于44个GO类别和122个代谢途径。此外,在35 238条unigene中共搜索到4 428个SSR位点,二核苷酸的SSR数目最多(1 906条),其次为三核苷酸(1 762条)。这些信息为毛葡萄功能基因、相关候选基因的发掘以及分子标记辅助育种提供了重要依据。

Transcriptome analysis of Vitis quinquangularis Rehd leaves was performed via a newly developed high-throughput sequencing technology. A total of 35 238 unigenes were generated with 1 081 nt of average length and 1 735 nt of unigene N50 after filtering and assembly of original reads. A total of 26 751 unigenes annotated with databases of non-redundant protein sequence（Nr）,Swiss-Prot,Kyoto Encyclopedia of Genes and Genomes（KEGG） databases and Clusters of Orthologous Groups（COG）and available at NCBI as references. 8 487 unigenes were not found in any databases. The species distribution pattern showed that 74.48% of the unique sequences had top matches to sequences from Vitis vinifera. Unigenes were classified into 25 classes through COG databases. Through GO classification and KEGG pathway enrichment analysis,all of these differentially expressed unigenes were classified into 44 GO terms and 122 metabolism pathways,respectively. In addition,4 428 potential SSR loci were detected from 35 238 unigene. Of them,tri-nucleotide repeats were the most abundant（1 906）,followed by trinucleotide（1 762） repeats. This study provides a foundation for further characterizing the functional genes in Vitis quinquangularis Rehd.