Mitochondrial genome structural characteristics and phylogenetic relationships of Dysomma anguillare
-
摘要: 【目的】分析前肛鳗线粒体基因组结构特征与系统发育关系,为前肛鳗的分类鉴定及种质资源现状评估提供理论依据。【方法】采用高通量测序技术获得前肛鳗线粒体基因组序列,分析其基因组成和结构特征,结合GenBank已公布的近缘种鱼类线粒体基因组序列,基于蛋白编码基因(PCGs)序列相似性使用最大似然法构建系统发育进化树,分析该鱼类在鳗鲡目中的亲缘关系及进化地位。【结果】前肛鳗线粒体基因组序列全长16690 bp,包含13个PCGs、22个tRNA、2个rRNA(12S rRNA和16S rRNA)及2个非编码区(D-loop和OL),碱基组成具有明显的A/T偏好性和反G偏倚,其中D-loop区AT含量最高(65.56%)。ATG是PCGs中最常见的起始密码子,6个基因以不完全密码子T-和TA-作为终止密码子。22个tRNA中仅tRNA-Ser(AGN)因缺失二氢尿嘧啶臂无法折叠成典型的三叶草形,且在t RNA-Leu(UUR)中识别到与哺乳动物线粒体转录终止因子(m TERF)结合位点高度相似的基序5'-TGGCAGAGCCTGG-3'。12S rRNA和16S rRNA的二级结构均由多茎环组成,且后者较前者更复杂。16S rRNA的结构域Ⅳ中存在与原核生物23S rRNA肽基转移酶中心(PTC)同源的保守多分支环(CML)。D-loop区中识别了扩展终止序列区(ETAS)、中央保守区(CSB-F、CSB-E和CSB-D)和保守序列区(CSB-1、CSB-2和CSB-3)。基于PCGs序列相似性构建的系统发育进化树显示,前肛鳗与寄生鳗、软泥鳗和考柯氏合鳃鳗的亲缘关系较近。【结论】前肛鳗线粒体基因组结构与大多数硬骨鱼类相似,长度介于鳗鲡目鱼类线粒体基因组长度范围之间,系统发育分析结果支持将前肛鳗归为合鳃鳗科前肛鳗属的分类地位。Abstract: 【Objective】The mitochondrial genome structural characteristics and phylogenetic relationships of Dy-somma anguillare were investigated so as to provide theoretical basis for species identification and germplasm resource as-sessment of this fish.【Method】The complete mitogenome of D.anguillare was obtained by high-throughput sequencing technology in this study.The gene composition and structure characteristics were analyzed,based on the mitochondrial ge-nome sequence of related fish published by GenBank,the phylogenetic evolutionary tree was constructed using the maxi-mum likelihood method based on the sequence similarity of protein-coding genes (PCGs) to analyze the relationship and evolutionary status of the fish in Anguilliformes.【Result】The total length of mitochondrial genome of D.anguillare was16690 bp,including 13 PCGs,22 tRNA genes,2 rRNA (12S rRNA and 16S rRNA) and 2 non-coding regions (D-loop and OL).The base composition showed obvious noticeable A/T preference and anti-G-bias.The content of AT in D-loop re-gion was the highest (65.56%).ATG was the most common start codon in PCGs.Six genes used incomplete codons T-and TA-as stop codons.Only tRNA-Ser(AGN) could not fold into the typical clover shape due to the absence of dihydroura-cil arm among the 22 tRNAs.The motif 5'-TGGCAGAGCCTGG-3'was identified in tRNA-Leu(UUR),which was highly similar to the binding site of mammalian mitochondrial transcription termination factor (mTERF).The secondary struc-tures of 12S rRNA and 16S rRNA were composed of multiple stem-loops,with the latter more complex than the former.Domain VI of 16S rRNA contained a conserved multibranched loop (CML) homologous to the prokaryotic 23S rRNA peptidyl transferase center (PTC).In D-loop region,extended termination sequence regions (ETAS),central conserved re-gions (CSB-F,CSB-E and CSB-D) and conserved sequence regions (CSB-1,CSB-2 and CSB-3) were identified.The phylogenetic tree constructed based on PCGs sequence similarity demonstrated that the D.anguillare was closely related to Simenchelys parasitica,Ilyophis brunneus and Synaphobranchus kaupii.【Conclusion】The mitogenomic structure of D.anguillare is similar to those of most bony fishes,the total length of the mitochondrial genome is between the range of An-guilliformes fishes,and the phylogenetic relationships supports to place D.anguillare in Synaphobranchidae,Dysomma.
-
Keywords:
- Dysomma anguillare /
- mitochondrial genome /
- structure and characteristics /
- phylogeny
-
-
陈大刚,张美昭.2015.中国海洋鱼类[M].青岛:中国海洋大学出版社.[Chen D G,Zhang M Z.2015.Marine fishes of China[M].Qingdao:China Ocean University Press.] 陈四海,区又君,李加儿.2011.鱼类线粒体DNA及其研究进展[J].生物技术通报,(3):13-20.[Chen S H,Ou Y J,Li J E.2011.Mitochondrial DNA and its progresses in fishes[J].Biotechnology Bulletin,(3):13-20.]doi: 10.13560/j.cnki.biotech.bull.1985.2011.03.033. 丁旭,齐鑫,尹绍武.2012.基于线粒体D-loop基因探讨花鳗鲡的群体遗传多样性及其种群进化历史[J].海洋科学,36(5):117-123.[Ding X,Qi X,Yin S W.2012.Genetic variation and population evolutionary history of the giant mottled eel (Anguilla marmorata) based on the mitochon-drial D-loop gene[J].Marine Sciences,36(5):117-123.] 赫崇波,曹洁,刘卫东,周遵春,葛陇利,高祥刚,王效敏.2007.圆斑星鲽及相关种类线粒体DNA控制区结构分析[J].遗传,29(7):829-836.[He C B,Cao J,Liu W D,Zhou Z C,Ge L L,Gao X G,Wang X M.2007.Structure analysis of mtDNA control region of spotted halibut(Verasper variegatus) and its related species[J].Heredi-tas,29(7):829-836.]doi: 10.16288/j.yczz.2007.07.012. 卢伙胜,欧帆,颜云榕,张军晓.2009.应用氮稳定同位素技术对雷州湾海域主要鱼类营养级的研究[J].海洋学报,31(3):167-174.[Lu H S,Ou F,Yam Y R,Zhang J X.2009.Study on trophic level of main fishes in the Leizhou Bay with stable nitrogen isotope techniques[J].Acta Oceano-logica Sinica,31(3):167-174.]doi: 10.3321/j.issn:0253-4193.2009.03.019. 廖波,王天明.2003.RNA二级结构的最小自由能算法[J].生物数学学报,18(3):364-368.[Liao B,Wang T M.2003.Minimal free energy algorithm of the secondary structure of RNA[J].Journal of Biomathematics,18(3):364-368.]doi: 10.3969/j.issn.1001-9626.2003.03.020. 刘焕章.2002.鱼类线粒体DNA控制区的结构和进化——以鳑鲏鱼类为例[J].自然科学进展,12(3):266-270.[Liu H Z.2002.The structure and evolution of mitochondrial DNA control region in fishes:A case study of bitterlings[J].Progress in Natural Science,12(3):266-270.]doi: 10.3321/j.issn:1002-008X.2002.03.008. 刘凯,冯晓宇,马恒甲,谢楠.2020.钱塘江三角鲂线粒体基因组测序及其结构特征分析[J].浙江农业学报,32(9):1591-1608.[Liu K,Feng X Y,Ma H J,Xie N.2020.Com-plete sequence and gene organization of mitochondrial genome of Megalobrama terminalis from Qiantang River[J].Acta Agriculturae Zhejiangensis,32(9):1591-1608.]doi: 10.3969/j.issn.1004-1524.2020.09.08. 刘凯,冯晓宇,吴燕琴,储忝江,谢楠.2021.瓯江高体鳑鲏线粒体基因组测序及结构特征分析[J].农业生物技术学报,29(6):1182-1197.[Liu K,Feng X Y,Wu Q Y,Chu TJ,Xie N.2021.Sequencing and structural characteristics analysis of mitochondrial genome in Rhodeus ocellatus from Ou River[J].Journal of Agricultural Biotechnology,29(6):1182-1197.]doi: 10.3969/j.issn.1674-7968.2021.06.016. 柳淑芳,吴仁协,朱玲,庄志猛.2010.小黄鱼(Larimichthys polyactis)线粒体基因组结构与特征[J].海洋与湖沼,41(6):885-894.[Liu S F,Wu R X,Zhu L,Zhuang Z M.2010.Complete sequence and gene organization of mito-chondrial DNA of the small yellow croaker Larimichthys polyactis[J].Oceanologia et Limnologia Sinica,41(6):885-894.] 沈世杰.1982.台湾鱼类志[M].台北:国立台湾大学动物学系.[Shen S J.1982.Fishes of Taiwan[M].Taipei:Acta Zoologica,National Taiwan University.] 沈世杰.1984.台湾鱼类检索[M].台北:南天书局.[Shen S J.1984.Taiwan fishes retrieval[M].Taipei:Nantian Bookstore.] 申欣,田美,孟学平,程汉良,阎斌伦.2014.鳗鲡目鱼类线粒体蛋白质编码基因易位及系统演化关系分析[J].海洋学报,36(4):73-81.[Shen X,Tian M,Meng X P,Cheng H L,Yan B L.2014.Eels mitochondrial protein-coding genes translocation and phylogenetic relationship analyses[J].Acta Oceanologica Sinica,36(4):73-81.]doi: 10.3969/j.issn.0253-4193.2014.04.009. 宋洁,张小芳,刁雪淘,金梅.2008.线粒体DNA 12S rRNA、16SrRNA研究进展[J].安徽农学通报,14(9):43-48.[Song J,Zhang X F,Diao X T,Jin M.2008.Research progress of mitochondrial DNA 12S rRNA and 16S rRNA[J].Anhui Agricultural Science Bulletin,14(9):43-48.]doi: 10.3969/j.issn.1007-7731.2008.09.017. 张波,唐启升.2003.东、黄海六种鳗的食性[J].水产学报,27(4):307-314.[Zhang B,Tang Q S.2003.Feeding habits of six species of eels in East China Sea and Yellow Sea[J].Journal of Fisheries of China,27(4):307-314.]doi: 10.3321/j.issn:1000-0615.2003.04.004. 张春光,唐文乔,刘东,张振玲,张世义.2010.中国动物志硬骨鱼纲鳗鲡目背棘鱼目[M].北京:科学出版社:305-307.[Zhang C G,Tang W Q,Liu D,Zhang Z L,Zhang SY.2010.Fauna Sinica(Osteichthyes Anguilliformes Notacanthiformes)[M].Beijing:Science Press.] 张莉,聂刘旺.2007.龟鳖类线粒体全基因组的比较研究[J].生命科学研究,11(3):258-262.[Zhang L,Nie L W.2007.Comparative study on the complete mitochondrial genome of turtles[J].Life Science Research,11(3):258-262.]doi: 10.3969/j.issn.1007-7847.2007.03.013. 赵卓,刘晨阳,瓮青芬,王保海,翟卿.2023.茶六斑褐锦斑蛾Sorita pulchella线粒体基因组特征与系统发育分析[J].河南农业大学学报,57(2):277-287.[Zhao Z,Liu C Y,Weng Q F,Wang B H,Zhai Q.2023.Characterization of the mitochondrial genome and phylogenetic analysis of Sorita pulchella[J].Journal of Henan Agricultural Univer-sity,57(2):277-287.]doi: 10.16445/j.cnki.1000-2340.20221110.00. 杨蕊,田思泉,高春霞,戴黎斌,王士聪.2020.浙江南部近海前肛鳗肌肉脂质去除对其稳定同位素测定结果的影响[J].中国水产科学,27(9):1085-1094.[Yang R,Tian SQ,Gao C X,Dai L B,Wang S C.2020.Effects of lipid removal on the stable isotopes of Dysomma anguillaris in the offshore waters of southern Zhejiang[J].Journal of Fishery Sciences of China,27(9):1085-1094.]doi: 10.3724/SP.J.1118.2020.20027. 俞存根,陈全震,陈小庆,宁平,郑基.2010.舟山渔场及邻近海域鱼类种类组成和数量分布[J].海洋与湖沼,41(3):410-417.[Yu C G,Chen Q Z,Chen X Q,Ning P,Zheng J.2010.Species composition and quantitative distribution of fish in the Zhoushan fishing ground and its adjacent waters[J].Oceanologia et Limnologia Sinica,41(3):410-417.] Boore J L.1999.Animal mitochondrial genomes[J].Nucleic Acids Research,27(8):1767-1780.doi: 10.1093/nar/27.8.1767.
Broughton R E,Milam J E,Roe B A.2001.The complete sequence of the zebrafish(Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochon-drial DNA[J].Genome Research,11(11):1958-1967.doi: 10.1101/gr.156801.
Cannone J J,Subramanian S,Schnare M N,Collett J R,D'Souza L M,Du Y S,Feng B,Lin N,Madabusi L V,Müller K M,Pande N,Shang Z D,Yu N,Gutell R R.2002.The comparative RNA web(CRW) site:An online database of comparative sequence and structure informa-tion for ribosomal,intron,and other RNAs[J].BMC Bio-informatics,3:2.doi: 10.1186/1471-2105-3-2.
Chen J N,López J A,LavouéS,Miya M,Chen W J.2014.Phy-logeny of the Elopomorpha(Teleostei):Evidence from six nuclear and mitochondrial markers[J].Molecular Phyloge-netics and Evolution,70:152-161.doi: 10.1016/j.ympev.2013.09.002.
Clayton D A.1982.Replication of animal mitochondrial DNA[J].Cell,28(4):693-705.doi: 10.1016/0092-8674(82)90049-6.
Clayton D A.1991.Nuclear gadgets in mitochondrial DNAreplication and transcription[J].Trends in Biochemical Sciences,16(3):107-111.doi: 10.1016/0968-0004(91)90043-U.
Dierckxsens N,Mardulyn P,Smits G.2017.NOVOPlasty:De nove assembly of organelle genomes from whole genome form whole genome data[J].Nucleic Acids Research,45(4):e18.doi: 10.1093lnarlgkw955.
Dornburg A,Friedman M,Near T J.2015.Phylogenetic analy-sis of molecular and morphological data highlights uncer-tainty in the relationships of fossil and living species of Elopomorpha(Actinopterygii:Teleostei)[J].Molecular Phy-logenetics and Evolution,89:205-218.doi: 10.1016/j.ympev.2015.04.004.
Fernandez-silva P,Martinez-azorin F,Micol V,Attardi G.1997.The human mitochondrial transcription termination factor(mTERF) is a multizipper protein but binds to DNAas a monomer,with evidence pointing to intramolecular leucine zipper interactions[J].The EMBO Journal,16(5):1066-1079.doi: 10.1093/emboj/16.5.1066.
Fernández-silva P,Enriquez J A,Montoya J.2003.Replication and transcription of mammalian mitochondrial DNA[J].Experimental Physiology,88(1):41-56.doi: 10.1113/eph8802514.
Forey P L,Littlewood T J,Ritchie P,Meyer A.1996.Interrela-tionships of elopomorph fishes[M]//Stiassny M L J,Parenti L R,Johnson G D.The Interrelationships of Fishes.San Diego:Academic Press.
Guindon S,Gascuel O.2003.A simple,fast,and accurate algo-rithm to estimate large phylogenies by maximum likeli-hood[J].Systematic Biology,52(5):696-704.doi: 10.1080/10635150390235520.
Hemmer-Hansen J,Hüssy K,Baktoft H,Huwer B,Bekkevold D,Haslob H,Herrmann J P,Hinrichsen H H,Krumme U,Mosegaard H,Nielsen E E,Reusch T B H,Storr-Paulsen M,Velasco A,von Dewitz B,Dierking J,Eero M.2018.Genetic analyses reveal complex dynamics within a marine fish management area[J].Evolutionary Applica-tions,12(4):830-844.doi: 10.1111/EVA.12760.
Inoue J G,Miya M,Tsukamoto K,Nishida M.2001.Complete mitochondrial DNA sequence of Conger myriaster (Teleostei:Anguilliformes):Novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for Anguilliform families[J].Journal of Molecular Evolu-tion,52(4):311-320.doi: 10.1007/s002390010161.
Inoue J G,Miya M,Tsukamoto K,Nishida M.2004.Mitoge-nomic evidence for the monophyly of elopomorph fishes(Teleostei) and the evolutionary origin of the leptocepha-lus larva[J].Molecular Phylogenetics and Evolution,32(1):274-286.doi: 10.1016/j.ympev.2003.11.009.
Iwasaki W,Fukunaga T,Isagozawa R,Yamada K,Maeda Y,Satoh T P,Sado T,Mabuchi K,Takeshima H,Miya M,Nishida M.2013.MitoFish and MitoAnnotator:A mito-chondrial genome database of fish with an accurate and automatic annotation pipeline[J].Molecular Biology and Evolution,30(11):2531-3540.doi: 10.1093/molbev/mst141.
Kerpedjiev P,Hammer S,Hofacker I L.2015.Forna(forcedirected RNA):Simple and effective online RNA secondary structure diagrams[J].Bioinformatics,31(20):3377-3379.doi: 10.1093/bioinformatics/btv372.
Lee W J,Conroy J,Howell W H,Kocher T D.1995.Structure and evolution of teleost mitochondrial control regions[J].Journal of Molecular Evolution,41(1):54-66.doi: 10.1007/BF00174041.
Lowe T M,Eddy S R.1997.tRNAscan-SE:A program for improved detection of transfer RNA genes in genomic sequence[J].Nucleic Acids Research,25(5):955-964.doi: 10.1093/nar/25.5.955.
LüZ M,Zhu K H,Jiang H,Lu X T,Liu B J,Ye Y Y,Jiang LH,Liu L Q,Gong L.2019.Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes[J].International Journal of Biological Macromolecules,135:609-618.doi: 10.1016/j.ijbiomac.2019.05.139.
Martin M.2011.Cutadapt removes adapter sequences from high-throughput sequencing reads[J].Embnet Journal,17(1):10-12.
Nelson J S.2006.Fishes of the world (fourth edition)[M].Hoboken,New Jersey:John Wiley&Sons,Inc.
Obermiller L E,Pfeiler E.2003.Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences[J].Molecular Phylogenetics and Evolu-tion,26(2):202-214.doi: 10.1016/s1055-7903(02)00327-5.
Ojala D,Montoya J,Attardi G.1981.tRNA punctuation model of RNA processing in human mitochondrial[J].Nature,290:470-474.doi: 10.1038/290470a0.
Perna N T,Kocher T D.1995.Patterns of nucleotide composi-tion at fourfold degenerate sites of animal mitochondrial genomes[J].Journal of Molecular Evolution,41(3):353-358.doi: 10.1007/BF00186547.
Polacek N,Mankin A S.2005.The ribosomal peptidyl transferase center:Structure,function,evolution,inhibition[J].Critical Reviews in Biochemistry and Molecular Biology,40(5):285-311.doi: 10.1080/10409230500326334.
Posada D,Crandall K A.1998.Modeltest:Testing the model of DNA substitution[J].Bioinformatics,14(9):817-818.doi: 10.1093/bioinformatics/14.9.817.
Robins C R,Bethesda A F S,Bailey R M,Bond C E,Brooker J R,Lachner E A.1980.A list of common and scientific names of fishes from the United States and Canada(Fourth Edition)[M].Bethesda,Maryland,USA:Ameri-can Fishe-ries Society Special Publication.
Roe A B,Ma D P,Wilson R K,Wong J F.1985.The complete nucleotide sequence of the Xenopus laevis mitochondrial genome[J].Journal of Biological Chemistry,260(17):9759-9774.
Sambrook J,Fritsch E F,Maniatis T.1982.Molecular cloning:A laboratory manual[M].New York:Cold Spring Harbor Laboratory Press.
Santini F,Kong X H,Sorenson L,Carnevale G,Mehta R S,Alfaro M E.2013.A multi-locus molecular timescale for the origin and diversification of eels(Order:Anguillifor-mes)[J].Molecular Phylogenetics and Evolution,69(3):884-894.doi: 10.1016/j.ympev.2013.06.016.
SbisàE,Tanzariello F,Reyes A,Pesole G,Saccone C.1997.Mammalian mitochondrial D-loop region structural analy-sis:Identification of new conserved sequences and their functional and evolutionary implications[J].Gene,205(1-2):125-140.doi: 10.1016/s0378-1119(97)00404-6.
Shadel G S,Clayton D A.1997.Mitochondrial DNA mainte-nance in vertebrates[J].Annual Review of Biochemistry,66:409-435.doi: 10.1146/annurev.biochem.66.1.409.
Sharma M R,Koc E C,Datta P P,Booth T M,Spremulli L L,Agrawal R K.2003.Structure of the mammalian mito-chondrial ribosome reveals an expanded functional role for its component proteins[J].Cell,115(1):97-108.doi: 10.1016/s0092-8674(03)00762-1.
Tamura K,Stecher G,Peterson D,Filipski A,Kumar S.2013.MEGA6:Molecular evolutionary genetics analysis ver-sion 6.0[J].Molecular Biology and Evolution,30(12):2725-2729.doi: 10.1093/molbev/mst197.
Tanaka M,Ozawa T.1994.Strand asymmetry in human mito-chondrial DNA mutations[J].Genomics,22(2):327-335.doi: 10.1006/geno.1994.1391.
Wang Y M,Zhang F Y,Zhao M,Ma C Y,Zhang L Z,Ma L B.2019.The complete mitochondrial genome of Dysomma anguillare(Anguilliformes,Synaphobranchidae) with phylogenetic consideration[J].Mitochondrial DNA Part B,4(1):1688-1689.doi: 10.1080/23802359.2019.1604103.
Xia X.1996.Maximizing transcription efficiency causes codon usage bias[J].Genetics,144(3):1309-1320.doi: 10.1093/genetics/144.3.1309.
Zhang K,Zhu K H,Liu Y F,Zhang H,Gong L,Jiang L H,Liu L Q,LüZ M,Liu B J.2021.Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes[J].Scien-tific Reports,11:1-14.doi: 10.1038/s41598-021-81622-9.
计量
- 文章访问数: 65
- HTML全文浏览量: 4
- PDF下载量: 21