奇异双身虫线粒体基因组测定及其密码子偏好性分析

【目的】为确定奇异双身虫线粒体基因组基本结构特征并探究奇异双身虫分类地位，同时了解双身虫科物种的密码子偏好性。【方法】采用二代高通量测序技术获得奇异双身虫线粒体基因组序列，通过MITOS在线网页对线粒体基因组序列进行注释并通过PhyloSuite (version1.2.2)软件对其结构进行分析，同时对奇异双身虫及其他8种双身虫科物种的线粒体蛋白质编码基因的密码子组成情况及密码子偏好性进行分析。【结果】奇异双身虫的线粒体基因组序列长度为15 713 bp(大非编码区未测全)，A+T含量为68.7%，表现出明显的AT偏向。系统发育树结果显示，基于现有数据双身虫科物种聚为一支，支持双身虫科物种的单系性。对双身虫科物种的密码子使用偏好进行分析，结果指出双身虫科有效密码子数(ENC)范围为30.632-37.495；相对同义密码子使用值(RSCU)>1的密码子共有18个，偏好以碱基U(T)结尾。PR2-plot分析结果显示T的使用频率高于A，G的使用频率高于C，突变和选择等因素均可对密码子的使用偏好产生一定的影响。中性绘图分析显示奇异双身虫和马口鱼拟双身虫受突变压力的影响分别为61.89%和51.31%，其余7种双身虫均受突变压力的影响小于50%。【结论】双身虫科密码子偏好性存在略微差异，但都受突变压力、自然选择和碱基组成的共同影响。【意义】本研究可以为后续的系统进化研究提供重要依据。

Determination of mitochondrial genome and analysis of codon preference of Diplozoon paradoxum (Nordmann, 1832)

【Objective】To determine the basic structural features of the mitochondrial genome, explore the taxonomic status of Diplozoon paradoxum (Nordmann, 1832), and to understand the codon preferences in Diplozoidae species.【Methods】The mitochondrial genome sequence of D. paradoxum was obtained by the second generation high-throughput sequencing technologies. The mitochondrial genome sequence was annotated by MITOS Web Server, and its structure was analyzed by PhyloSuite (version1.2.2). Then, we analyzed the codon composition and preference of mitochondrial protein-coding genes on nine species of Diplozoidae.【Results】The mitochondrial genome sequence of D. paradoxum was 15,713 bp in length (the large non-coding region was not fully sequenced), the AT content of D. paradoxum was 68.7%, which had an obvious AT bias. Based on the available data, the results of phylogenetic tree showed that all species of Diplozoidae were grouped into one branch, and revealed that Diplozoidae was a monophyletic group. The analysis of codon usage preferences showed that the effective codon number (ENC) ranged from 30.632 to 37.495 in Diplozoidae. The relative synonymous codon usage (RSCU) values of 18 codons were > 1 in Diplozoidae, and the all codons of that ending with the U(T). The analysis of PR2-plot showed that the frequency of T was higher than that of A, and the frequency of G was higher than that of C. The codon usage preferences were affected by mutation and selection in some extent. The analysis of neutral mapping showed that the effects of mutation pressure on D. paradoxum and P. opsariichthydis were 61.89% and 51.31%, respectively, while the effects of mutation pressure on other seven species were below 50%.【Conclusion】Codon preference of Diplozoidae had slight differences, and all of codon preference of Diplozoidae were affected by mutation pressure, natural selection, and base composition.【Significance】This study can provide an important basis for the follow-up study of system evolution.