广西华珊瑚蛇线粒体基因组全序列测定与分析

Mitochondrial Genome Sequencing of Sinomicrurus peinani

本研究对眼镜蛇科广西华珊瑚蛇(Sinomicrurus peinani)线粒体基因组序列进行测定与分析,并探究其与近缘种的系统发育关系。结果表明,广西华珊瑚蛇线粒体基因组是一条全长19477 bp的环状DNA,基因组碱基构成为A(33.4%)、T(28.1%)、C(26.6%)和G(11.9%)。共编码38个基因,包含2个核糖体RNA(rRNA)基因、22个转移RNA(tRNA)基因、13个蛋白质编码基因及1个线粒体基因控制区(D-loop)。13个蛋白质编码基因均采用AUG作为起始密码子,UAA和UGA作为终止密码子;蛋白质编码基因编码频率较高的氨基酸分别为亮氨酸(Leu)、异亮氨酸(Ile)、苏氨酸(Thr)和丝氨酸(Ser);相对密码子使用度(RSCU)频率最高的4个密码子依次是CGA、UGA、CUA和CCA。22个tRNA,除tRNASer(一臂两环)外其他均可形成典型三叶草结构。基于眼镜蛇科线粒体基因组系统发育分析结果表明,与广西华珊瑚蛇关系最密切的是中华珊瑚蛇(Sinomicrurus macclellandi),其次是孟加拉眼镜蛇(Naja kaouthia)与眼镜王蛇(Ophiophagus hannah)。

[Objectives]To determine the mitochondrial gene sequence of Sinomicrurus peinani,a new species of cobra family,and explore its phylogenetic relationship with related species.[Methods]We used the online software Feature Extract 1.2L server(http://www.cbs.dtu.dk/services/FeatureExtract).The protein coding regions of mitochondrial genome of S.peinani were extracted,and the proportions of four bases and base deviation of different genes were calculated by bioedit(Donath 2012).The online software tRNAscan-SE 2.0 was used(http://lowelab.ucsc.edu/Trnascan SE)to predict the type and secondary structure of tRNA according to antisense codon and isotype model(Lowe et al.1997),Conventional methods were used to analyze the base composition of triplet codon position,codon usage,the influence of base composition on codon preference and parity preference,and MEGA7.0 was used to construct phylogenetic tree.[Results]The results showed that the mitochondrial genome of S.peinani was a 19477 bp circular DNA molecule,and the genomic bases were A(33.4%),T(28.1%),C(26.6%)and G(11.9%),which encode 38 genes including 2 ribosomal RNA(rRNA)genes,22 transfer RNA(tRNA)genes,13 protein coding genes and 1 replication origin gene(D-loop).The 13 protein coding genes use AUG as the starting codon and UAA and UGA as the termination codon.The amino acids with high coding frequency of protein coding genes were Leu,Ile,Thr and Ser,respectively;The four codons with the highest frequency of Relative synonymous condon usage(RSCU)were CGA,UGA,CUA and CCA.All 22 tRNAs except tRNASer(with one arm and two rings)could form typical clover structure.[Conclusion]Phylogenetic analysis showed that S.macclellandi was most closely related to the taxonomic status of S.peinani,followed by Naja kaouthia and Ophiophagus hannah(Fig.2,3,6).