虾虎鱼类线粒体全基因组序列结构特征分析及系统发育关系探讨

doi:10.3724/SP.J.1005.2013.01391

遗传 ›› 2013, Vol. 35 ›› Issue (12): 1391-1402.doi: 10.3724/SP.J.1005.2013.01391

虾虎鱼类线粒体全基因组序列结构特征分析及系统发育关系探讨

金逍逍, 孙悦娜, 王日昕, 汤达, 赵盛龙, 徐田军

浙江海洋学院海洋科学与技术学院, 鱼类分子遗传与免疫进化实验室, 舟山 316000

收稿日期:2013-05-22 修回日期:2013-08-07 出版日期:2013-12-20 发布日期:2013-11-25
通讯作者: 徐田军, 副教授, 研究方向：鱼类分子免疫及分子进化。 E-mail:tianjunxu@163.com
作者简介:金逍逍, 硕士, 专业方向：鱼类分子系统学。E-mail: jinxiaoxiaoyy@163.com
基金资助:
国家自然科学基金项目(编号：31272661)和浙江省自然科学基金项目(编号：LY13C040001)资助

Characteristics and phylogenetic analysis of mitochondrial genome in the gobies

JIN Xiao-Xiao, SUN Yue-Na, WANG Ri-Xin, TANG Da, ZHAO Sheng-Long, XU Tian-Jun

Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan 316000, China

Received:2013-05-22 Revised:2013-08-07 Online:2013-12-20 Published:2013-11-25
Contact: tianjun Xu E-mail:tianjunxu@163.com

摘要/Abstract

摘要：

虾虎鱼类体态变异大、体型小、种类多, 形态鉴定及谱系分类较为困难。为深入开展虾虎鱼类的鉴定、分类及遗传进化等研究, 文章对已获得的26种虾虎鱼线粒体全基因组进行分析。结果发现, 虾虎鱼类线粒体基因组的基因组成及排列模式与大多数脊椎动物线粒体基因组特征基本一致; 由于不同物种的控制区存在不同数量的重复序列而导致基因组序列长度存在明显的差异; 26种虾虎鱼线粒体全基因组序列及不同基因中A+T的含量均超过50%, 并存在碱基G偏倚现象。基于37个编码基因序列, 利用Kimura双参数法计算遗传距离, 发现矛尾刺虾虎鱼与斑尾刺虾虎鱼、斑纹舌虾虎鱼与钝吻舌虾虎鱼分别为同种异名。通过对26种虾虎鱼线粒体基因组控制区序列的比较, 识别了终止结合序列区、中央保守区及保守序列区。利用26种虾虎鱼线粒体基因组的36个编码基因序列构建系统发育树, 发现部分聚类结果不同于传统的形态学分类方式, 虾虎鱼科中的5个亚科出现了明显的分化, 近盲虾虎鱼亚科、背眼虾虎鱼亚科、瓢虾虎鱼亚科亲缘关系较近而聚成一大支, 然后与拟虾虎鱼亚科种类形成姐妹类群, 虾虎鱼亚科与其它的4个亚科亲缘关系较远, 单独成为一个类群。根据分子钟估算结果推测虾虎鱼科物种可能起源于始新世晚期至渐新世时段, 在中新世进一步分化为具有现代表征的虾虎鱼种类。

关键词: 虾虎鱼类, 线粒体基因组, 结构特征, 系统发育基因组学

Abstract:

The vast number of species, small size and high variation of morphology make the morphological identification and classification of gobies very difficult. In this study, the complete mitochondrial genome (mitogenome) of 26 species of gobies was analyzed, aiming at accumulating the molecular information on the identification, classification and molecular evolution of gobies. The results showed that the gene composition and arrangement of mitogenome of gobies are similar to most vertebrates. Due to various degrees of repetitive sequences in the control region, the mitogenome of 26 gobies exhibits a great variation in length. The A+T content of the mitogenome is greater than 50% and the lowest frequency is for G among the four bases. Thirty-seven coding gene sequences were used to calculate the average Kimura 2-parameter genetic distance of 26 species of gobies. Acanthogobius hasta and A. ommaturus, Glossogobius olivaceus and G. circumspectus were synonyms, respectively. By comparing the control region sequences of 26 gobies, the terminal associated sequences, central conserved sequence block and conserved sequence block were identified, respectively. Thirty-six coding gene sequences of 26 gobies were used to construct the phylogenetic tree and the results were different from the traditional morphological classification. The five subfamilies of Gobiidae were obviously evolved: Amblyopinae, Oxudercinae and Sicydiinae were clustered into a group and then formed a sister group with Gobionellinae; the fishes of Gobiinae had distant relationship with the four subfamilies and formed a group alone. Molecular clock analysis estimated that gobies probably originated in the late Eocene to Oligocene time and further evolved into modern characteristic gobies in the Miocene.

Key words: Gobies, mitochondrial genome, structure characteristic, phylogenomic analysis

金逍逍孙悦娜王日昕汤达赵盛龙徐田军. 虾虎鱼类线粒体全基因组序列结构特征分析及系统发育关系探讨[J]. 遗传, 2013, 35(12): 1391-1402.

JIN Xiao-Xiao, SUN Yue-Na, WANG Ri-Xin, TANG Da, ZHAO Sheng-Long, XU Tian-Jun. Characteristics and phylogenetic analysis of mitochondrial genome in the gobies[J]. HEREDITAS, 2013, 35(12): 1391-1402.

参考文献

[1] 伍汉霖, 钟俊生. 中国动物志: 硬骨鱼纲鲈形目 (五) 虾虎鱼亚目. 北京: 科学出版社, 2008. <\p>

[2] 孙希福. 基于形态学和分子生物学资料探讨中国沿海10种虾虎鱼类的系统发育关系. 青岛: 中国海洋大学, 2009. <\p>

[3] Thacker CE. Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). Mol Phylogenet Evol, 2003, 26(3): 354–368. <\p>

[4] Akihito, Iwata A, Kobayashi T, Ikeo K, Imanishi T, Ono H, Umehara Y, Hamamatsu C, Sugiyama K, Ikeda Y, Saka-moto K, Fumihito A, Ohno S, Gojobori T. Evolutionary aspects of gobioid fishes based upon a phylogenetic analysis of mitochondrial cytochrome b genes. Gene, 2000, 259(1-2): 5–15. <\p>

[5] Wang HY, Tsai MP, Dean J, Lee SC. Molecular phylogeny of gobioid fishes (Perciformes: Gobioidei) based on mi-tochondrial 12S rRNA sequences. Mol Phylogenet Evol, 2001, 20(3): 390–408. <\p>

[6] Thacker CE, Hardman MA. Molecular phylogeny of basal gobioid fishes: Rhyacichthyidae, Odontobutidae, Xenisthmidae, Eleotridae (Teleostei: Perciformes: Gobioidei). Mol Phylogenet Evol, 2005, 37(3): 858–871. <\p>

[7] Thacker CE. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and in-vestigation of diversification and character evolution. Copeia, 2009, 2009, (1): 93−104. <\p>

[8] Keith P, Lord C, Lorion J, Watanabe S, Tsukamoto K, Couloux A, Dettai A. Phylogeny and biogeography of Sicydiinae (Teleostei: Gobiidae) inferred from mitochondrial and nuclear genes. Mar Biol, 2011, 58(2): 311–326. <\p>

[9] Lord C, Lorion J, Dettai A, Watanabe S, Tsukamoto K, Cruaud C, Keith P. From endemism to widespread distribution: phylogeography of three amphidromous Sicyopterus species (Teleostei: Gobioidei: Sicydiinae). Mar Ecol, 2012, 455: 269–285. <\p>

[10] Jeon HB, Choi SH, Suk HY. Exploring the utility of partial cytochrome c oxidase subunit 1 for DNA barcoding of gobies. J Anim Syst, Evol Diver, 2012, 28(4): 269–278. <\p>

[11] 李林, 梁宏伟, 李忠, 罗相忠, 呼光富, 张志伟, 朱媛媛, 皱桂伟. 瓦氏黄颡鱼线粒体全基因组序列分析及系统进化. 遗传, 2011, 33(6): 627–635. <\p>

[12] Nelson JS. Fishes of the world. 4d ed. New York: John Wiley and Sons, 2006. <\p>

[13] Kim IC, Kweon HS, Kim YJ, Kim CB, Gye MC, Lee WO, Lee YS, Lee JS. The complete mitochondrial genome of the javeline goby Acanthogobius hasta (Perciformes, Gobii-dae) and phylogenetic considerations. Gene, 2004, 336(2): 147–153. <\p>

[14] Bucciarelli G, Di Filippo M, Costagliola D, Alvarez-Valin F, Bernardi G, Bernardi G. Environmental genomics: a tale of two fishes. Mol Biol Evol, 2009, 26(6): 1235–1243. <\p>

[15] Kim YJ, Kweon HS, Kim IC, Lee JM, Lee JS. The com-plete mitochondrial genome of the floating goby, Gym-nogobius petschiliensis (Perciformes, Gobiidae). Mol Cells, 2004, 17(3): 446–453. <\p>

[16] Liu ZZ, Wang CT, Ma LB, He AY, Yang JQ, Tang WQ. Complete mitochondrial genome of the mudskipper Bo-leophthalmus pectinirostris (Perciformes, Gobiidae): Re-petitive sequences in the control region. Mitochondr DNA, 2012, 23(1): 31–33. <\p>

[17] Maeda K, Mukai T, Tachihara K. A new species of am-phidromous goby, Stiphodon alcedo, from the Ryukyu Archipelago (Gobiidae: Sicydiinae). Cybium, 2011, 35(4): 285–298. <\p>

[18] Chiang TY, Chen IS, Lin HD, Chang WB, Ju YM. Complete mitochondrial genome of Sicyopterus japonicus (Perciformes, Gobiidae). Mitochondr DNA, 2013, 24(3): 191–193. <\p>

[19] Ki JS, Jung SO, Hwang DS, Lee YM, Lee JS. Unusual mitochondrial genome structure of the freshwater goby Odontobutis platycephala: rearrangement of tRNAs and an additional non-coding region. J Fish Biol, 2008, 73(2): 414–428. <\p>

[20] Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, Shirai SM, Nishida M. Major patterns of higher teleo-stean phylogenies: a new perspective based on 100 com-plete mitochondrial DNA sequences. Mol Phylogenet Evol, 2003, 26(1): 121–138. <\p>

[21] Waddell PJ, Cao Y, Hauf J, Hasegawa M. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with spe-cial reference to the positions of hedgehog, armadillo, and elephant. Syst Biol, 1999, 48(1): 31–53. <\p>

[22] Guindon S, Gascuel O. A simple, fast, and accurate algo-rithm to estimate large phylogenies by maximum likeli-hood. Syst Biol, 2003, 52(5): 696–704. <\p>

[23] Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. MrBayes 3.2: efficient Bayesian phy-logenetic inference and model choice across a large model space. Syst Biol, 2012, 61(3): 539–542. <\p>

[24] Miller PJ. The osteology and adaptive features of Rhyacichthys aspro (Teleostei: Gobioidei) and the classification of gobioid fishes. J Zool, 1973, 171(3): 397–434. <\p>

[25] Meganathan PR, Pagan HJT, McCulloch ES, Stevens RD, Ray DA. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera. Gene, 2012, 492(1): 121–129. <\p>

[26] 杨超, 汪青雄, 黄原, 肖红. 棕头鸥线粒体基因组全序列测定与分析. 遗传, 2012, 34(11): 1434–1446. <\p>

[27] 柯杨, 黄原, 雷富民. 黑尾地鸦线粒体基因组序列测定与分析. 遗传, 2010, 32(9): 951–960. <\p>

[28] Shackelton LA, Parrish CR, Holmes EC. Evolutionary ba-sis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol, 2006, 62(5): 551– 563. <\p>

[29] Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature, 1981, 290(5806): 470–474. <\p>

[30] Hebert PDN, Cywinska A, Ball SL, DeWaard JR. Bio-logical identifications through DNA barcodes. Proc Royal Soc B: Biol Sci, 2003, 270(1512): 313–321. <\p>

[31] 秦克静, 姜志强. 斑尾复鰕虎鱼和矛尾复鰕虎鱼同物异名的探讨. 大连水产学院学报, 1987, (2): 37–39. <\p>

[32] 宋娜, 高天翔, 孙希福, 柳本卓. 矛尾复虾虎鱼物种命名有效性探讨. 动物分类学报, 2010, 35(2): 352–359. <\p>

[33] Cheng YZ, Jin XX, Shi G, Wang RX, Xu TJ. Genetic di-versity and population structure of miiuy croaker popula-tions in East China Sea revealed by the mitochondrial DNA control region sequence. Biochem Syst Ecol, 2011, 39(4-6): 718–724. <\p>

[34] 郭新红, 刘少军, 刘巧, 刘筠. 鱼类线粒体DNA研究新进展. 遗传学报, 2004, 31(9): 983–1000. <\p>

[35] Liu Y, Cui ZX. The complete mitochondrial genome se-quence of the cutlassfish Trichiurus japonicus (Percifor-mes: Trichiuridae): Genome characterization and phy-logenetic considerations. Mar Genomics, 2009, 2(2): 133– 142. <\p>

[36] Catanese G, Manchado M, Infante C. Evolutionary relat-edness of mackerels of the genus Scomber based on com-plete mitochondrial genomes: Strong support to the rec-ognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species. Gene, 2010, 452(1): 35–43. <\p>

[37] Lee WJ, Conroy J, Howell WH, Kocher TD. Structure and evolution of teleost mitochondrial control region. J Mol Evol, 1995, 41(1): 54–66. <\p>

[38] Hoese DF, Gill A. Phylogenetic relationships of eleotridid fishes (Perciformes: Gobioidei). Bull Mar Sci, 1993, 52(1): 415–440. <\p>

[39] Nelson JS. Fishes of the world. 3d ed. New York: John Wiley and Sons, 1994. <\p>

[40] Akihito, Iwata A, Sakamoto K, Ikeda Y. Suborder Go-bioidei. In: Nakabo T. Fishes of Japan with pictorial keys to the species. Tokyo: Tokai University Press, 1993: 997– 1116, 1355–1392. <\p>

[41] Patterson C. Osteichthyes: Teleostei. In: Benton MJ. The Fossil Record 2. London: Chapman and Hall, 1993: 622– 656. <\p>

[42] Frost GA. A comparative study of the otoliths of the Neopterygian fishes (continued). Ann Mag Nat Hist, 1929, 10(4): 120–130. <\p>

[43] Haines T. Walking with Beasts: A Prehistoric Safari. New York: Dorling Kindersley Publishing Inc., 1999.<\p>

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

虾虎鱼类线粒体全基因组序列结构特征分析及系统发育关系探讨

Characteristics and phylogenetic analysis of mitochondrial genome in the gobies

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	匡卫民, 于黎. 基因组时代线粒体基因组拼装策略及软件应用现状[J]. 遗传, 2019, 41(11): 979-993.
[2]	孙长斌, 张曦. 超级增强子研究进展[J]. 遗传, 2016, 38(12): 1056-1068.
[3]	李雪娟, 黄原, 雷富民. 山鹧鸪属鸟类线粒体基因组的比较及系统发育研究[J]. 遗传, 2014, 36(9): 912-920.
[4]	王章群, 解增言, 蔡应繁, 舒坤贤, 黄飞飞. 系统发育基因组学研究进展[J]. 遗传, 2014, 36(7): 669-678.
[5]	董文鸽郭宪国金道超薛士鹏秦凤 Simon Song, Stephen C. Barker, Renfu Shao. 虱目裂化线粒体基因组研究进展[J]. 遗传, 2013, 35(7): 847-855.
[6]	杨超，汪青雄，黄原，肖红. 棕头鸥线粒体基因组全序列测定与分析[J]. 遗传, 2012, 34(11): 1434-1446.
[7]	李林，梁宏伟，李忠，罗相忠，呼光富，张志伟，朱媛媛，邹桂伟. 瓦氏黄颡鱼线粒体全基因组序列分析及系统进化[J]. 遗传, 2011, 33(6): 627-635.
[8]	柯杨，黄原，雷富民. 黑尾地鸦线粒体基因组序列测定与分析[J]. 遗传, 2010, 32(9): 951-960.
[9]	陈念，赖小平. 眼镜王蛇线粒体基因组全序列分析[J]. 遗传, 2010, 32(7): 719-725.
[10]	蒋文枰，李家乐，郑润玲，汪桂玲. 褶纹冠蚌线粒体基因组全序列分析[J]. 遗传, 2010, 32(2): 153-162.
[11]	陈芳建，俞红，樊璠，吕建新. 线粒体基因组D-Loop区基因多态性与2型糖尿病的相关性[J]. 遗传, 2009, 31(3): 265-272.
[12]	童晓梅，梁羽，王威，徐树青，郑晓光，汪建，于军. 藏鸡线粒体全基因组序列的测定和分析[J]. 遗传, 2006, 28(7): 769-777.
[13]	于黎，张亚平. 系统发育基因组学——重建生命之树的一条迷人途径[J]. 遗传, 2006, 28(11): 1445-1450.
[14]	危文亮，王汉中，刘贵华. 植物细胞质雄性不育性与育性恢复的分子生物学研究进展[J]. 遗传, 2005, 27(4): 651-658.
[15]	张晓梅，单祥年，施燕峰，张海军，李健，郑爱玲. 小麂线粒体基因组全序列的测定和分析[J]. 遗传, 2004, 26(6): 849-853.