基于美洲和中国大鲵转录组序列的线粒体基因组组装及其遗传多样性分析
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摘要
为利用高通量测序数据开展线粒体基因组研究,基于高通量第2代测序技术获得了美洲大鲵(Cryptobranchus alleganiensis)转录组数据,以近缘物种的线粒体全基因组为参考序列,利用MITObim软件对其组装,并进行环化、注释和分析,采用邻接法(NJ法)构建美洲大鲵线粒体基因组序列的系统进化树。结果表明:美洲大鲵线粒体全基因组序列长度为16 358 bp,包含13个蛋白编码基因(PCG)、22个tRNA基因、2个rRNA基因和1个控制区。同时利用该项技术对中国大鲵(Andrias davidianus)转录组数据也提取线粒体组数据,并构建大鲵属的系统进化树,结果表明中国大鲵与日本大鲵(Andrias japonicus)亲缘性较近,获取的美洲大鲵与参考的美洲大鲵(Gen Bank登录号GQ368662)聚为一类。这一研究提示中国大鲵和美洲大鲵起源不同,遗传距离大。
In order to extract the mitochondrial genome sequence information from RNA-Seq data,the transcriptome genomic data of Cryptobranchus alleganiensis with a close reference sequence was used by MITObim software assembles.A list of work such as assembles,cyclizes,annotates and analysis were conducted.The phylogenetic tree of the C.alleganiensis mitochondrial genome sequence was constructed by Neighbor-Joining(NJ method).The results showed that the length of mitochondrial genome sequence was 16 358 bp,including 13 protein coding genes(PCG),22 tRNA genes,2 rRNA genes and 1 control region.In order to proof this technology,mitochondrial genome sequence was also contracted from Chinese giant salamander(Andrias davidianus) transcriptome genomic data.Based on the assembled sequences,phylogenetic tree was built.The result showed that the Chinese giant salamander and Japanese giant salamander(Andrias japonicus) belonged to the same cluster,the reference C.alleganiensis and assembled mt DNA was involved in the same clade.These illustrated that Chinese giant salamander has a long genetic distance with the C.alleganiensis.
In order to extract the mitochondrial genome sequence information from RNA-Seq data,the transcriptome genomic data of Cryptobranchus alleganiensis with a close reference sequence was used by MITObim software assembles.A list of work such as assembles,cyclizes,annotates and analysis were conducted.The phylogenetic tree of the C.alleganiensis mitochondrial genome sequence was constructed by Neighbor-Joining(NJ method).The results showed that the length of mitochondrial genome sequence was 16 358 bp,including 13 protein coding genes(PCG),22 tRNA genes,2 rRNA genes and 1 control region.In order to proof this technology,mitochondrial genome sequence was also contracted from Chinese giant salamander(Andrias davidianus) transcriptome genomic data.Based on the assembled sequences,phylogenetic tree was built.The result showed that the Chinese giant salamander and Japanese giant salamander(Andrias japonicus) belonged to the same cluster,the reference C.alleganiensis and assembled mt DNA was involved in the same clade.These illustrated that Chinese giant salamander has a long genetic distance with the C.alleganiensis.
引文
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[3]WU Q L,LI Q,GU Y,et al.The complete mitochondrial genome of Taeniogonalos taihorina(Bischoff)(Hymenoptera:Trigonalyidae)reveals a novel gene rearrangement pattern in the Hymenoptera[J].Gene,2014,543(1):76-84.
[4]SIMON C,BUCKLEY T R,FRATI F,et al.Incorporating molecular evolution into phylogenetic analysis,and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA[J].Annual Review of Ecology Evolution&Systematics,2006,37(1):545-579.
[5]DOU W,WANG B J,WEI D D,et al.The complete mitochondrial genome of the citrus red mite Panonychus citri(Acari:Tetranychidae):high genome rearrangement and extremely truncated tRNAs[J].Bmc Genomics,2010,11(1):597.
[6]BALLARD J,RAND D.The population biology of mitochondrial DNA and its phylogenetic implications[J].Annual Review of Ecology Evolution&Systematics,2005,36(3):621-642.
[7]彭亮跃.中国大鲵基础生物学及其进化的研究[D].长沙:湖南师范大学,2010.
[8]HAHN C,BACHMANN L,CHEVREUX B.Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads:a baiting and iterative mapping approach[J].Nucleic Acids Research,2013,41(13):e129.
[9]CAMACHO C,COULOURIS G,AVAGYAN V,et al.BLAST+:architecture and applications[J].BMC Bioinformatics,2009,10(1):1-9.
[10]LOHSE M,DRECHSEL O,BOCK R.Organellar genome DRAW(OGDRAW):a tool for the easy generation of highquality custom graphical maps of plastid and mitochondrial genomes[J].Current Genetics,2007,52(5/6):267-274.
[11]DIXON M T,HILLIS D M.Ribosomal RNA secondary structure:compensatory mutations and implications for phylogenetic analysis[J].Molecular Biology&Evolution,1993,10(1):256-267.
[12]POSADA D,CRANDAL K A.Modeltest:testing the model of DNA substitution[J].Bioinformatics,1998,14(9):817-818.
[13]LANAVE C,PREPARATA G,SACCONE C,et al.A new method for calculating evolutionary substitution rates[J].J Mol Evo,1984,20(1):86-93.
[14]连总强,滚双宝,李力,等.基于第二代测序技术兰州鲇线粒体基因组全序列测定与分析[J].水生生物学报,2017,41(2):334-345.
[15]屠云洁,束婧婷,章明,等.狼山鸡保种群不同世代线粒体DNA条形码变化规律研究[J].扬州大学学报(农业与生命科学版),2016,37(3):54-57.
[16]LEE W J,KOCHER T D.Complete sequence of a sea lamprey(Petromyzon marinus)mitochondrial genome:early establishment of the vertebrate genome organization[J].Genetics,1995,139(2):873.
[17]HAO W,FAN S,WEI H,et al.Effective extraction and assembly methods for simultaneously obtaining plastid and mitochondrial genomes[J].Plos ONE,2014,9(9):e108291.
[18]YE F,SAMUEL D C,CLARK T,et al.High-throughput sequencing in mitochondrial DNA research[J].Mitochondrion,2014,17(7):157-163.
[19]SHARMA M R,KOC E C,DATTA P P,et al.Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins[J].Cell,2003,115(1):97.
[20]LINDAHL T.DNA repair enzymes[J].Annual Reviews in Biochemistry,1982,51(1):61-87.
[21]LINDAHL T.Instability and decay of the primary structure of DNA[J].Nature,1993,362(6422):709-715.
[22]张乃心.双翅目昆虫线粒体基因组测序通用引物设计及葱蝇线粒体基因组测序与分析[D].重庆:重庆师范大学,2013.
[23]陶峰勇,王小明,郑合勋,等.中国大鲵4种群的遗传结构和地理分化[J].动物学研究,2005,26(2):162-167.