日本鼓虾与鲜明鼓虾线粒体基因组全序列的分析比较

Comparison and analysis of Alpheus japonicus and A.distinguendus complete mitochondrial genome sequences

首先通过基因组DNA的提取、通用引物PCR扩增和长PCR扩增,从而获得日本鼓虾(Alpheus japonicus)的线粒体DNA;应用鸟枪法和引物步移法测序,获得了日本鼓虾的线粒体基因组全序列。结合GenBank线粒体基因组数据库中鲜明鼓虾(A.distinguendus)的线粒体基因组,比较分析了鼓虾线粒体基因组的基本特征、基因排列、蛋白质编码基因、选择压力和差异位点等。研究结果表明,在日本鼓虾线粒体基因组中共存在9对基因的重叠。日本鼓虾线粒体基因组全长16 487bp,较鲜明鼓虾线粒体基因组(15 700bp)长,主要是由于最大非编码区的长度存在差异。日本鼓虾与鲜明鼓虾线粒体基因组均编码37个基因,且37个基因的基因排列完全一致;与泛甲壳动物线粒体基因组的原始排列相比,仅出现1个转运RNA基因(trnE)的易位和倒位。2个鼓虾线粒体基因组蛋白质编码基因的起始密码子和终止密码子存在差异。除了cob基因外,其余12个蛋白质编码基因所编码氨基酸的数目均完全相同。鼓虾线粒体基因组13个线粒体蛋白质编码基因的Ka/Ks比值都远远低于1,显示出较强的负选择。在15个主编码基因中,nad5基因的变异位点数最多,其次是nad4基因和lrRNA基因。因此,nad5,nad4和lrRNA基因可以作为备选的分子标记,用于分析鼓虾不同物种和群体之间的生物多样性。

The mitochondrial genomic DNA of Alpheus japonicus was obtained by genomic DNA extraction combined with universal primers PCR and long PCR amplification.The complete mitochondrial genome sequence was sequenced using shotgun and primer-walking strategies.Comparative analyses were done combined with A.distinguendus mitochondrial genome,including the basic characteristics,gene order,protein-coding genes,selection pressure,and different sites and so on.The results show that overlapping is found in nine pairs genes of A.japonicus mitochondrial genome.The A.japonicus mitochondrial genome is 16 487 bp in length and is longer than A.distinguendus mitochondrial genome（15 700 bp）,mainly due to the length difference of the largest non-coding region.The mitochondrial genomes of A.japonicus and A.distinguendus both contain 37 genes.Gene order of the A.japonicus and A.distinguendus mitochondrial genomes is identical.The translocation of one transfer RNA gene（trnE） involving inversion is found in 2 Alpheus mitochondrial genomes when compared with the pancrustacean ground pattern.There are differences in the usage of start codon and stop codon in protein-coding genes of 2 Alpheus mitochondrial genomes.Except for the cob gene,the numbers of amino acids encoded by the remaining 12 protein-coding genes are identical.The Ka/Ks ratio of all 13 mitochondrial protein coding genes is much lower than 1,indicating a strong negative selection.In 15 major coding genes,nad5 has the largest number of different loci,followed by nad4 and lrRNA genes,can be used as alternative molecular markers to analyze biodiversity among Alpheus species and populations.