基于线粒体D-loop区和COI基因序列研究2个禾花鲤群体和野生鲤群体的遗传多样性与系统进化关系

Genetic diversity and phylogenetic relationship among two populations of Procypris merus and wild carp based on mtDNA D-loop region and COI gene sequences

利用线粒体D-loop区和COI基因序列分析了全州禾花鲤(Quanzhou Procypris merus)、融水禾花鲤(Rongshui P.merus)和野生鲤鱼群体的遗传多样性和系统进化关系。基于D-loop区序列分析结果表明:序列长度为927~930 bp,共统计变异位点53个;A、T、G、C核苷酸平均含量分别为33.4%、32.9%、14%和19.7%,A+T(66.3%)明显高于G+C(33.7%);总体的单倍型数(h)、单倍型多样性(Hd)和核苷酸多样性(π)分别为40个、0.95和0.0083;遗传分化指数(Fst)为0.22459。基于COI基因序列分析结果显示:序列长度为897~899 bp,共统计变异位点33个;A、T、G、C核苷酸平均含量分别为26.7%、28.5%、17.8%和27%,且A+T(55.2%)高于G+C(44.8%);总体的h为25个,Hd为0.91,π为0.00316;Fst值为0.19143。在3个群体内和群体间遗传距离分别在0.003~0.009和0.003~0.01,远小于种群分类水平0.05。分子方差分析(AMOVA)结果表明,77.54%(D-loop)和80.86%(COI)变异来自群体间变异,22.46%(D-loop)和19.14%(COI)来自群体内变异。单倍型进化树和网络图显示,全州禾花鲤和野鲤群体均存在单独聚为一支的单倍型,而融水群体未出现单独成支现象。研究表明,线粒体D-loop区作为反映3个群体间遗传多样性的灵敏度要高于COI基因,并且3个群体均属于高单倍型多样性和高核苷酸多样性。综上,3个群体间出现了较为明显的分化现象。

Mitochondrial D-loop region and COI sequences were used to analyze the genetic diversity and phylogenetic relationships among the populations of Quanzhou Procypris merus,Rongshui P.merus and Wild Carp.The results of sequence analysis based on D-loop region indicated that the sequence length was 927-930 bp,which contained 53 variable sites.The average content of A,T,G and C nucleotides in the sequences were 33.4%,32.9%,14% and 19.7%,respectively.A+T(66.3%)was significantly higher than G+C(33.7%)in D-loop sequences.Overall haplotype(h),haplotype diversity(Hd)and nucleotide diversity(π)of D-loop sequences were 40,0.95 and 0.0083,respectively.Then the genetic differentiation index(Fst)was 0.22459.The results of sequence analysis based on COI showed that the sequence length was 897-899 bp,which contained 33 variable sites.The average content of A,T,G and C nucleotides in COI sequence were 26.7%,28.5%,17.8% and 27%,respectively.A+T(55.2%)was significantly higher than G+C(44.8%)in COI sequences.Overall haplotype(h)was 25,haplotype diversity(Hd)was 0.91,nucleotide diversity(π)was 0.00316.Then the genetic differentiation index(Fst)was 0.19143.The genetic distances within the three populations and between the populations were 0.003~0.009 and 0.003~0.01,respectively,which were much smaller than the population classification level of 0.05.Molecular analysis of variance(AMOVA)showed that 77.54%(D-loop)and 80.86%(COI)variation were identified from populations,and 22.46%(D-loop)and 19.14%(COI)were from intra-population variation.The haplotype phylogenetic tree and the network map showed that haplotypes were clustered together in Quanzhou Procypris merus and the wild carp population,while the population of Rongshui Procypris merus did not show a separate branch.Studies have shown that the sensitivity of the mitochondrial D-loop region as a reflection of genetic diversity among the three populations is higher than that of the COI gene,and all three populations belong to high haplotype diversity and high nucleotide diversity.Overall,there was a more obvious differentiation among the three populations.