马口鱼全基因组简单重复序列特征分析与多态性标记开发

Characteristics and polymorphic markers development of whole genome simple sequence repeat of Opsariichthys bidens

为开发马口鱼(Opsariichthys bidens)多态性简单重复序列(simple sequence repeat,SSR)标记,利用微卫星识别工具(microsatellite identification tool,MISA)搜索统计马口鱼全基因组SSR,采用生物信息学方法对其分布特征进行比较分析;选取39个三核苷酸SSR位点设计引物进行多态性检测。结果显示:马口鱼全基因组中SSR总数量为304870个,占全基因组长度的0.10%;二核苷酸SSR为马口鱼基因组中的主要重复类型。5种重复类型SSR数量为二核苷酸SSR>四核苷酸SSR>三核苷酸SSR>六核苷酸SSR>五核苷酸SSR。内含子区SSR数量最多,为93380个;5′非翻译区SSR数量最少,为622个。各区域SSR数量分布情况为内含子区>基因间隔区>启动子区>3′非翻译区>编码区>5′非翻译区。编码区数量最多的是三核苷酸SSR,而其他5个区域最多的是二核苷酸SSR。各重复类型拷贝数分布范围为5~350,主要集中在5~30。通过筛选得到15对多态性引物,在野生群体马口鱼中共检测到106个等位基因,观测杂合度为0.125~0.813,期望杂合度为0.359~0.862,多态信息含量(PIC)为0.339~0.830,其中12对引物具有高度多态性(PIC>0.5)。这些微卫星标记为马口鱼的种群遗传多样性分析、亲缘关系鉴定等研究提供了基础数据。

In order to develop polymorphic simple sequence repeat(SSR)markers,the SSR were searched and computed in the genome of Opsariichthys bidens by microsatellite identification tool(MISA).The SSR distribution characteristics were analyzed by bioinformatics methods,and 39 tri-nucleotide loci were selected for primers design and polymorphism detection.The total SSR number detected in the O.bidens genome were 304870,which accounted for 0.10%of the whole genome length.Di-nucleotide SSR was the dominant repeat type in the genome of O.bidens.The number of 5 SSR repeat types was di->tetra->tri->hexa->penta-nucleotide.The introns had the highest number of SSR,with the number of 93380,while 5′UTR had the smallest number of SSR,with the number of 622.The order of SSR number of 6 regions was introns>intergenics>promoter>3′UTR>CDS>5′UTR.Tri-nucleotide SSR was the dominant repeat type in coding sequence,but di-nucleotide SSR was the dominant repeat type in the other 5 regions.The repeat number ranged from 5 to 350,mainly distributed in 5 to 30.Fifteen pairs of polymorphic primers were screened,and 106 alleles were detected in a wild population of O.bidens,the observed heterozygosity was 0.125 to 0.813,and the expected heterozygosity was 0.359 to 0.862,the polymorphism information content(PIC)was 0.339 to 0.830,12 pairs of primers were highly polymorphic(PIC>0.50).These microsatellite markers provided basic data for population genetic diversity and parentage determination of O.bidens.