食蟹豆齿鳗线粒体基因组结构特征及系统进化分析

The mitochondrial genomic characteristics and phylogenetic relationship analysis of Pisodonophis cancrivorus(Anguilliformes,Ophichthidae)

食蟹豆齿鳗(Pisodonophiscancrivorus)是我国东南沿海重要的渔获种类之一。本研究采用高通量测序技术对采自于舟山近海的食蟹豆齿鳗线粒体基因组进行了测定,并对其结构特征及系统发育关系进行了分析。食蟹豆齿鳗线粒体DNA序列全长为17650bp,4种碱基含量分别为A(31.72%)、G(15.58%)、T(26.26%)和C(26.44%),表现出明显的反G偏倚和A+T富集现象。与已发表的蛇鳗科鱼类相似,其线粒体部分基因由于自然选择的作用,发生了串联复制–随机丢失(tandem duplication-randomloss,TDRL)事件,导致ND6基因和tRNA-Glu(E)转移到tRNA-Thr(T)和tRNA-Pro(P)之间,并且ND6基因上游出现了另一个长度为966bp的控制区,两个控制区呈现独立演化的特征。13个蛋白质编码基因中分别存在2种启动子(ATG、GTG)和4种终止子(TAG、TAA、TA-、T--),且仅COI基因以GTG作为起始密码子。编码的3824个氨基酸中,亮氨酸(Leu)含量最高而半胱氨酸(Cys)含量最低。22种tRNA的二级结构中存在17处碱基错配,且仅tRNA-SerAGY(S)由于缺少二氢尿嘧啶臂(DHU臂)无法折叠形成典型的三叶草结构。长度为21bp的轻链复制起始区(originofL-strandreplication region,OL)位于“WANCY”基因簇内,其发夹型二级结构(hairpin secondary structure)的3'端具有与爬行动物类似的保守功能基序3'-GGCGG-5'。将17种蛇鳗科鱼类的线粒体12个蛋白质编码基因序列去除终止密码子之后进行串联,基于Kimura双参数模型计算种间遗传距离为0.128~0.297。使用最大似然法(maximum likelihood,ML)和贝叶斯法(Bayesian inference,BI)构建系统发育树,显示了蛇鳗科鱼类复杂的演化关系,食蟹豆齿鳗位于进化树的基部,与短尾蛇鳗(Ophichthusbrevicaudatus)和艾氏蛇鳗(O.evermanni)亲缘关系最近,是该类群中较晚发生遗传分化的种类。

Pisodonophis cancrivorus is an important fish species in the southeast coast of China.In this study,the complete mitochondrial genome of P.cancrivorus was obtained by high-throughput sequencing technique,as well as the structural characteristics and phylogenetic relationships were also analyzed.The total length of the complete mitochondrial DNA is 17650bp,and the base compositions are A(31.72%),G(15.58%),T(26.26%) and C(26.44%),respectively,showing an obvious anti-G bias and A+T preference.Similar to the published mitogenomes of Ophichthidae species,some genes have undergone a tandem duplication-random loss(TDRL) event due to the natural selection,causing the ND6 gene and its conjoint tRNA-Glu(E) to be translocated between tRNA-Thr(T) and tRNA-Pro(P).Besides,another D-loop region with length of 966bp is located upstream of the ND6 gene,and these two D-loop regions show a trend of independent evolution.There are two start codons(ATG,GTG) and four stop codons(TAG,TAA,TA-,T--) among the 13 protein-coding genes(PCGs),and only COI gene is initiated with GTG.In the total of 3 824 encoded amino acids,the content of Leu is the highest,while the content of Cys is the lowest.There are 17 DNA mismatches in the secondary structures of 22 tRNAs.All tRNAs can form the clover-leaf structures,excepting tRNA-Ser~(AGY)(S)because of lacking the DHU arm.The origin of L-strand replication region(O_L) with the length of 21bp is situated in the “WANCY”region,and the conserved motif 3'-GGCGG-5' is detected in the 3' end of its hairpin secondary structure.The sequences of 12 PCGs(without ND6) are concatenated by removing stop codons,and the interspecific genetic distances of 17 Ophichthidae fishes are calculated to be 0.128-0.297 based on the Kimura two-parameter(K2P) model.The phylogenetic trees constructed by the maximum likelihood(ML) and Bayesian inference(BI) methods show a complex evolutionary relationship of Ophichthidae fishes.P.cancrivorus is located at the base of the phylogenetic tree and closely related to Ophichthus brevicaudatus and O.evermanni,suggesting that it may diverge later than other snake eels.