Bioinformatics identification, analysis of gene structure and expression characters on lineage-specific genes of grapevine | 葡萄谱系特有基因生物信息学识别、基因结构与表达特性分析

Chinese. 以葡萄全基因组29 971蛋白序列为查询序列,与包括葡萄在内的31个已测序植物蛋白序列、TIGR和NCBI数据库中的EST和非冗余蛋白质序列进行非同源性比对分析,保留E值大于0.01的序列,去除重复序列、转座子和注释不准确的基因序列,保留的非同源基因识别为葡萄谱系特有基因;并对谱系特有基因的结构和具有芯片表达信息的谱系特有基因的表达特性进行了分析。结果表明:共识别了2 009个葡萄谱系特有基因,与葡萄保守基因相比较,葡萄谱系特有基因平均外显子数量较少,为2个;平均外显子长度较短,为232 bp;平均内含子长度较长,为1 723 bp,与拟南芥、水稻等谱系特有基因结构特点相似,谱系特有基因可能具有相似的起源和进化模式。在47个具有芯片表达信息和相应UniGene信息的基因中,Vv04s0023g01710、Vv00s0187g00160、Vv17s0000g09800、Vv14s0083g00260分别在叶片、茎、细胞培养物、果实中相对表达量最高,相对表达量分别为2 120、2 282、5 566、1 428;有25个谱系特有基因仅在某一器官中表达,表明谱系特有基因具有器官特异性特点;分析34个谱系特有基因在4种非生物胁迫下基因表达情况,表明大部分基因表达受到明显抑制或不受诱导,推测非生物胁迫影响了这些谱系特有基因正常功能,也说明这些谱系特有基因较少参与非生物胁迫过程。

English. 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 lineage-specific 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.