Bioinformatics identification,analysis of gene structure and expression characters on lineage-specific genes of grapevine
LIANG Yinghai;CHEN Fei;WANG Gang;WANG Min;FENG Guanqiao;CHENG Zongming;College of Horticulture,Nanjing Agricultural University;Institute of Pomology,Academy of Agricultural Sciences of Jilin Province;
29 971 protein sequences in grapevine genome were queryed and blasted with 31 sequenced plant genomes( including grapevine genome),expressed sequence tags and non-redundant protein squences in TIGR and NCBI,and then genes with repeated sequences,false transposon and wrong annotations were removed. The remaining nonhomologous genes over E-value cutoff 0. 01 were identified as grapevine lineage-specific genes. The gene structure and expression characters of the lineage-specific genes with microarray expression data were analyzed. As a result,2 009 genes were identified as grapevine lineage-specific genes. Compared with grapevine conserved genes,grapevine lineage-specific genes had an average of 2 exons,which was less than that of grapevine conserved genes. The average exon length of grapevine lineage-specific genes was shorter than that of grapevine conserved genes. The average intron length of grapevine lineage-specific genes was longer than that of grapevine conserved genes. These structure properties of grapevine lineage-specific genes were similar to lineage-specific genes of Arabidopsis and Oryza sativa,suggesting that lineage-specific genes probably shared one common origin and evolution pattern. The relative expression quantities of Vv04s0023g01710,Vv00s0187g00160,Vv17s0000g09800,Vv14s0083g00260 were 2 120,2 282,5 566,1 428 in leaf,stem,cell culture and fruit respectively,and were highest among 47 lineagespecific genes with microarray expression data and corresponding UniGene information. There were 25 lineage-specific genes,which only expressed in one specific organ,suggesting that these genes owned the character of organ specificity expression. Under four abiotic stress conditions,many gene expressions among 34 lineage-specific genes were significantly depressed or not induced,showing that normal biological functions of lineage-specific genes were possibly affected by abiotic stress,or few lineage-specific genes were involved in response to abiotic stress.