基于16S rRNA基因部分序列的长江口虾虎鱼科鱼类系统分类

为了确定线粒体16S rRNA基因在长江口虾虎鱼科鱼类系统分类及物种鉴定中的作用,采用16S rRNA基因特异扩增测序及Gen Bank已有序列联合配对分析的方法,对长江口虾虎鱼科9属11种鱼类34个16S rRNA基因片段的序列进行比较和系统分类研究。统计分析显示,虾虎鱼科鱼类该片段的A含量明显高于其它3个碱基含量,A+T的平均含量高于G+C的平均含量,第3密码子位点G+C含量最高,其平均值为51.1%,变化范围为49.8%~53.2%。全部转换位点多于颠换位点,转换/颠换比值为1.45。依据Maximum Composite Likelihood模型,得出11种虾虎鱼科鱼类种间遗传距离平均值为0.151,种内为0.002,种间遗传距离是种内遗传距离的76倍。通过邻接法(Neighbor-joining,NJ)构建系统发育树,显示长江口虾虎鱼科鱼类为明显的单系群,并进一步佐证把传统形态分类中弹涂鱼科的青弹涂鱼(Scartelaos histiophorus)和大弹涂鱼(Boleophthalmus pectinirostris)及鳗虾虎鱼科的拉氏狼牙虾虎鱼(Odontamblyopus lacepedii)和红狼牙虾虎鱼(Odontamblyopus rubicundus)归属于虾虎鱼科的合理性。聚类结果显示红狼牙虾虎鱼和拉氏狼牙虾虎鱼聚在一起,其节点支持率达100%,两者可能为同种异名。本研究表明,线粒体16S rRNA基因序列作为分子标记对虾虎鱼科鱼类进行物种鉴定和系统分类是可行的,可为虾虎鱼类的亲缘关系分析提供基础资料。

Phylogenetic analysis of Gobiidae in the Yangtze Estuary based on partial sequence of Mitochondrial 16S rRNA

To determine the role of mitochondrial 16S rRNA genes in classification and identification of species,a total of 34 single individuals from 11 species pertaining to 9 genera of Gobiidae were barcoded by 16S rRNA,and compared with of Gobiidae species recorded in GenBank.Total genomic DNA was extracted from each sample using marine animal genome DNA extraction kit.PCR amplification was performed in total volume of 50μL of PCR mixture,and PCR products were purified and sequenced in single direction using an ABI PRISMTM 3 730 XL Automated Sequencer.By statistical analysis of MEGA 5 .0 software,the average content of A (30.6%)was significantly higher than that of other three bases,and the average content of A+T (52.3%)was higher than the G+C content (47.7%).The G+C content of the third position codon was higher than that of the other positions,whose average content was 51 .1% and the range was from 49 .8% to 53.2%.All transitional pairs (si)were slightly more than that of transversional pairs (sv),and the ratio (R=si/sv)was 1.45 .Based on Maximum Composite Likelihood model,the average distance pairwise-species and within-species was 0.151 and 0.002,respectively.The average distance pairwise-species was 76 times that of within-species.According to the neighbor joining (NJ)trees for all 34 sequences,it was demonstrated that Gobiidae in the Yangtze Estuary was a monophyletic group,which further confirmed that the classification of Scartelaos histiophorus and Boleophthalmus pectinirostris,Odontamblyopus lacepedii and Odontamblyopus rubicundus,as Gobiidae was reasonable.O.lacepedii and O.rubicundus were placed in the same clade with support of a high bootstrap value of 100%,indicating that these two species may be synonyms.Our results highlight that the information from 16S rRNA sequences can not only filter out the synonym of the same species,but also can be used to carry out effective identification for Gobiidae species,which further shows that 16S rRNA is feasible as classification barcode and can provide basis for phylogenetic relationship researches on Gobiidae.