蜱螨线粒体基因组串联重复序列DNA的分布与进化特征分析

Distribution and evolutionary characteristics of tandem repeat DNA in the mitochondrial genome of Acari

【目的】本研究旨在明确蜱螨线粒体基因组(mtDNA)串联重复序列(微卫星和长串联重复DNA)的分布规律和进化特征,为开发蜱螨分子标记和研究线粒体微卫星的功能提供基础数据。【方法】采用Microsatellite identification tool(MISA)和Tandem repeat finder等本地软件发掘蜱螨线粒体基因组串联重复序列DNA,分析其组成类型、分布规律和进化特征。【结果】本研究基于37科217种蜱螨线粒体基因组,鉴定获得1454个完美型线粒体微卫星(mtSSRs)和96个复合型微卫星。其中,完美型mtSSRs包含271个单碱基微卫星(SSR1)、127个双碱基微卫星(SSR2)、517个三碱基微卫星(SSR3)、323个四碱基微卫星(SSR4)、75个五碱基微卫星(SSR5)以及46个六碱基微卫星(SSR6)。分析发现,随着微卫星核心重复碱基数目的增加,其重复次数范围逐渐变小。蜱螨大多数mtSSRs倾向分布于线粒体电子传递链复合体Ⅰ所编码的nad4和nad5基因之中。同时,本文鉴定获得167个长串联重复序列(核心重复碱基数>6 bp),且50.3%分布于蛋白编码区。但核心重复基序较长的片段类型主要分布在特定物种的AT控制区。此外,革蜱属Dermacentor多数物种的线粒体基因组含有2个长串联重复序列区域。【结论】蜱螨线粒体基因组中三碱基微卫星和四碱基微卫星的数量最为丰富,且多分布于线粒体蛋白编码区域。同时,蜱螨线粒体微卫星存在长度多态性,且微卫星的变异与某些蜱虫的生物学特性密切相关。革蜱属近缘种间的线粒体基因组近期可能经历了复制、删除或重组事件。总之,本研究发掘的线粒体串联重复序列将为蜱螨物种鉴定、种群遗传多样性以及分子系统进化研究提供丰富的分子标记。

[Aim]This study aimed to investigate the distribution and evolutionary characteristics of mitochondrial DNA(mtDNA)microsatellite(SSR)and long tandem repeats(LTR)within the Acari group.This investigation will provide fundamental data for the development of molecular markers and functional research involving mitochondrial microsatellites.[Methods]The mitochondrial microsatellite(mtSSRs)and long tandem repeats of mites and ticks were mined using microsatellite identification tool(MISA)and tandem repeat finder,respectively.A comprehensive analysis was then carried out on composition,distribution patterns,and evolutionary characteristics of the tandem repeats.[Results]In total,1454 perfect mtSSRs and 96 complex mtSSRs were identified in 217 species of Acari,representing 37 families.Among these,there were 271 mononucleotide repeats(SSR1),127 dinucleotide repeats(SSR2),517 trinucleotide repeats(SSR3),323 tetranucleotide repeats(SSR4),75 pentanucleotide repeats(SSR5),and 46 hexanucleotide repeats(SSR6).The results showed that as the motif length of SSR increased,the number of repeat times decreased.The majority of mtSSRs in Acari were found in the nad4 and nad5 protein domains,which are encoded by mitochondrial complex I.Additionally,167 long tandem repeats(LTR,core repeat base number>6 bp)were found,with 50.3%of them occurring in the coding region.Notably,the LTR with long core repeat units were found predominantly in the AT control region of specific species.Furthermore,most species in the Dermacentor genus exhibited two long repetitive regions in their mitochondrial genomes.[Conclusion]This study revealed that SSR3 and SSR4 are the most prevalent tandem repeats in the mitochondrial genome of Acari,and that they mainly appear in the mitochondrial protein-coding region.Additionally,SSR length polymorphism was observed in ticks and mites,and this variation in SSRs is strongly associated with various biological traits in ticks.The mitochondrial genomes of related species of Dermacentor may have recently undergone replication,deletion,or recombination events.In conclusion,the mitochondrial tandem repeats identified in this study will provide abundant molecular markers for the identification,population genetic diversity assessment,and molecular phylogenetic and evolutionary analysis of ticks and mites.