+高级检索
首页 > 过刊浏览>2022年第29卷第1期 >13-27. DOI:10.12264/JFSC2021-0084
PDF HTML阅读 XML下载 导出引用 引用提醒
七种骨舌鱼核糖体序列特征及遗传发育分析
作者:
作者简介:

杨叶欣(1980–),女,助理研究员,主要从事种质资源与生态安全研究.E-mail:yangyexin@163.com

中图分类号:

S917

基金项目:

农业农村部都市农业重点实验室开放基金项目(UA201910)； 广州市科技计划项目(201904010409)； 广东省现代农业产业技术体系创新团队建设项目(2021KJ150)； 国家淡水水产种质资源库项目(FGRC18537).


Characteristics of ribosomal gene of seven Osteoglossidae species and molecular phylogeny
Author:
  • YANG Yexin

    YANG Yexin

    Key Laboratory of Leisure Fisheries, Ministry of Agriculture and Rural Affairs , Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380 , China ；Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai 200240 , China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • LIU Yi

    LIU Yi

    Key Laboratory of Leisure Fisheries, Ministry of Agriculture and Rural Affairs , Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380 , China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • LIU Chao

    LIU Chao

    Key Laboratory of Leisure Fisheries, Ministry of Agriculture and Rural Affairs , Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380 , China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • SONG Hongmei

    SONG Hongmei

    Key Laboratory of Leisure Fisheries, Ministry of Agriculture and Rural Affairs , Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380 , China ；Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380 , China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • WANG Xuejie

    WANG Xuejie

    Key Laboratory of Leisure Fisheries, Ministry of Agriculture and Rural Affairs , Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380 , China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • MU Xidong

    MU Xidong

    Key Laboratory of Leisure Fisheries, Ministry of Agriculture and Rural Affairs , Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380 , China
    在期刊界中查找
    在百度中查找
    在本站中查找
  • 摘要
    • | |
  • 访问统计
    • |
  • 参考文献 [59]
    • |
  • 相似文献 [20]
    • | | |
  • 文章评论
    摘要:

    利用核糖体 DNA 序列探讨了骨舌鱼科(Osteoglossidae)高阶元的分子系统发育关系。采用分子标记技术, 分析测定了现存的 7 种骨舌鱼核糖体基因, 获得了巨骨舌鱼(Arapaima gigas)、尼罗异耳骨舌鱼(Heterotis niloticus)、 双须骨舌鱼(Osteoglossum bicirrhosum)、费氏骨舌鱼(O. ferreirai)、美丽硬仆骨舌鱼(Scleropages formosus)、乔氏硬仆骨舌鱼(S. jardinii)和硬仆骨舌鱼(S. leichardti)的 rDNA 全序列, 长度分别为 11714 bp、8957 bp、12057 bp、11556 bp、10377 bp、10724 bp 和 10725 bp, GC 碱基含量为 63.78%~66.13%。采用邻接法和贝叶斯推论法分别构建了系统进化树, 结果显示, 除 ITS1 外, 18S、ITS2、28S 和 18S+ITS1+5.8S+ITS2+28S 联合序列建树均与传统的分类相符合, 研究结果阐明了骨舌鱼科亚科、属和种间的分类关系, 核糖体 DNA 可作为骨舌鱼科的分子标记。

    Abstract:

    Osteoglossidae, a family of ancient fishes known as “living fossils,” has high economic, cultural, and scientific value. In this study, we analyzed the molecular phylogeny of higher-order elements in the Osteoglossidae family using ribosomal DNA sequences. The complete sequences of the ribosomal gene of Arapaima gigas, Heterotis niloticus, Osteoglossum bicirrhosum, O. ferreirai, Scleropages formosus, S. jardinii, and S. leichardti, obtained using second-generation and third-generation sequencing methods, were as follows: 11714 bp, 8957 bp, 12057 bp, 11556 bp, 10377 bp, 10724 bp, and 10725 bp, respectively. The base content of GC ranged from 63.78% to 66.13%. The lengths of 18S rDNA were 1835 bp; GC content ranged from 54.06% to 54.5%. The genetic distance ranged from 0.000 to 0.024, and the sequence identity varied from 97.52% to 100%. The lengths of ITS1 rDNA were between 598 bp and 871 bp; GC content ranged from 72.6% to 78.3%. The genetic distance ranged from 0.000 to 0.852, and the sequence identity varied from 38.34% to 99.5%. The lengths of 5.8S rDNA were 159 bp; GC content ranged from 57.23% to 57.86%. The genetic distance ranged from 0.000 to 0.019, and the sequence identity varied from 98.11% to 100%. The lengths of ITS2 rDNA were between 327 bp and 612 bp; GC content ranged from 70.34% to 80.07%. The genetic distance ranged from 0.000 to 0.799, and the sequence identity varied from 31.63% to 99.53%. The lengths of 28S rDNA were between 3996 bp and 4419 bp; GC content ranged from 62.42% to 65.69%. The genetic distance ranged from 0.000 to 0.066, and the sequence identity varied from 84.98% to 99.95%. The lengths of IGS rDNA were between 1815 bp and 4679 bp; GC content ranged from 63.73% to 71.52%. The genetic distance ranged from 0.001 to 1.877, and the sequence identity varied from 19.31% to 98.31%. The phylogenetic tree was constructed using the neighbor-joining method and Bayesian inference method on the 18S, ITS1, ITS2, and 28S single sequences and the 18S+ITS1+5.8S+ITS2+28S combined sequence. The results showed that the topological structure of the two trees was consistent. Moreover, this result is concordant with the traditional classification of seven species of bony tongue fish, except for ITS1, which can be used as a molecular marker of Osteoglossidae. Our findings provide data for the phylogenetic study of ancient fishes and to enrich the diversity and evolution mode research of fish using ribosomal RNA genes.

    参考文献
    [1] Weider L J,Elser J J,Crease T J,et al.The functional significance of ribosomal(r)DNA variation:Impacts on the evolutionary ecology of organisms[J].Annual Review of Ecology,Evolution,and Systematics,2005,36:219-242.
    [2] Hillis D M,Dixon M T.Ribosomal DNA:Molecular evolution and phylogenetic inference[J].The Quarterly Review of Biology,1991,66(4):411-453.
    [3] Appels R,Honeycutt R L.rDNA:Evolution over a billion years[M]//DNA Systematics.Boca Raton:CRC Press,1986:81-135.
    [4] Krawczyk K,Nobis M,Nowak A,et al.Phylogenetic implications of nuclear rRNA IGS variation in Stipa L.(Poaceae)[J].Scientific Reports,2017,7:11506.
    [5] Shapoval N A,Lukhtanov V A.Intragenomic variations of multicopy ITS2 marker in Agrodiaetus blue butterflies(Lepidoptera,Lycaenidae)[J].Comparative Cytogenetics,2015,9(4):483-497.
    [6] Bélanger-Lépine F,Leung C,Glémet H,et al.Balancing selection on the number of repeats in the ribosomal intergenic spacer present in naturally occurring yellow perch(Perca flavescens)populations[J].Genome,2018,61(1):1-6.
    [7] Normand A C,Packeu A,Cassagne C,et al.Nucleotide sequence database comparison for routine dermatophyte identification by internal transcribed spacer 2 genetic region DNA barcoding[J].Journal of Clinical Microbiology,2018,56(5):e00046-18.
    [8] Wu B S,Si L Z,Kong X Y,et al.The analysis of ITS1 characteristics of 11 species from 5 families and its application in phylogenetic research[J].Journal of Fisheries of China,2018,42(4):465-475.[武宝生,司李真,孔晓瑜,等.5科11种鱼类ITS1特征分析及其在系统分类研究中的适用性[J].水产学报,2018,42(4):465-475.]
    [9] West C,James S A,Davey R P,et al.Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species[J].Systematic Biology,2014,63(4):543-554.
    [10] Si L Z,Wu B S,Kong X Y,et al.Analysis of the GC content of ribosomal genes of 11 species of Perci-formes and comparison with other teleostean fishes[J].Journal of Fishery Sciences of China,2017,24(4):657-668.[司李真,武宝生,孔晓瑜,等.11种鲈形目鱼类的核糖体基因GC含量及其与硬骨鱼类的特征比较[J].中国水产科学,2017,24(4):657-668.]
    [11] Greenwood P,Rosen D,Weitzman S,et al.Phyletic studies of teleostean fishes,with a provisional classification of living forms[J].Bulletin of the American Museum of Natural History,1966,131(4):341-455.
    [12] Mu X D,Wang P X,Hu Y C,et al.Morphological structure and growth characteristics of juvenile Asian arowana(Scleropages formosus)[J].Journal of Fisheries of China,2010,34(9):1379-1386.[牟希东,王培欣,胡隐昌,等.亚洲龙鱼形态结构及幼鱼生长特性[J].水产学报,2010,34(9):1379-1386.]
    [13] Moreau M A,Coomes O T.Potential threat of the international aquarium fish trade to silver arawana Osteoglossum bicirrhosum in the Peruvian Amazon[J].Oryx,2006,40(2):152-160.[LinkOut]
    [14] Mu X D,Wang X J,Song H M,et al.Mitochondrial DNA as effective molecular markers for the genetic variation and phylogeny of the family Osteoglossidae[J].Gene,2012,511(2):320-325.
    [15] Rowley J J L,Emmett D A,Voen S.Harvest,trade and conservation of the Asian arowana Scleropages formosus in Cambodia[J].Aquatic Conservation:Marine and Freshwater Ecosystems,2008,18(7):1255-1262.
    [16] Mu X D,Hu Y C,Wang X J,et al.Genetic variability in cultured stocks of Scleropages formosus in mainland China revealed by microsatellite markers[J].Journal of Animal and Veterinary Advances,2011,10(5):555-561.
    [17] Mu X D,Liu Y,Wang X J,et al.Characterization of the mitochondrial genome and phylogeny of the black arowana(Osteoglossum ferreirai)[J].Biologia,2014,69(9):1222-1230.
    [18] Mu X D,Yang Y X,Liu Y,et al.Complete mitochondrial genome of northern spotted barramundi,Scleropages jardinii[J].Mitochondrial DNA,2015,26(5):698-699.
    [19] Gao B J,Zhang J.The complete mitochondrial genome of Scleropages formosus(Osteoglossiformes:Osteoglossidae)and phylogenetic studies of Osteoglossiformes[J].Conservation Genetics Resources,2017,9(2):265-268.
    [20] Austin C M,Tan M H,Croft L J,et al.Whole genome sequencing of the Asian arowana(Scleropages formosus)provides insights into the evolution of ray-finned fishes[J].Genome Biology and Evolution,2015,7(10):2885-2895.
    [21] Mu X D,Gu D G,Yang Y X,et al.Genetic diversity and phylogeny of the family Osteoglossidae by the nuclear 18S ribosomal RNA and implications for its conservation[J].Biochemical Systematics and Ecology,2013,51:280-287.
    [22] Duan Y N,Liu Y,Hu Y C,et al.Distribution regularity of microsatellites in Scleropages formosus genome[J].Chinese Agricultural Science Bulletin,2019,35(23):152-158.[段永楠,刘奕,胡隐昌,等.美丽硬仆骨舌鱼全基因组微卫星分布规律特征[J].中国农学通报,2019,35(23):152-158.]
    [23] Wang Q L,Liu Y,Song H M,et al.Development and primer selection of EST-SSR molecular markers based on transcriptome sequencing of Osteoglossum bicirrhosum[J].Freshwater Fisheries,2016,46(6):8-13.[王且鲁,刘奕,宋红梅,等.双须骨舌鱼转录组EST-SSR标记开发与引物筛选[J].淡水渔业,2016,46(6):8-13.]
    [24] Chase M W,Salamin N,Wilkinson M,et al.Land plants and DNA barcodes:Short-term and long-term goals[J].Philosophical Transactions of the Royal Society B:Biological Sciences,2005,360(1462):1889-1895.
    [25] Zhou Y,Du X L,Zheng X,et al.ITS2 barcode for identifying the officinal rhubarb source plants from its adulterants[J].Biochemical Systematics and Ecology,2017,70:177-185.
    [26] Gong L,Xu H,Li J,et al.Characterization of the first internal transcribed spacer of ribosomal DNA in Paralichthys olivaceus(♀)and P.dentatus(♂)hybrids[J].Journal of Fishery Sciences of China,2015,22(1):17-23.[龚理,徐晖,李军,等.褐牙鲆(♀)、夏鲆(♂)及其杂交子一代的ITS1序列特征分析[J].中国水产科学,2015,22(1):17-23.]
    [27] Gong L,Shi W,Yang M,et al.Non-concerted evolution in ribosomal ITS2 sequence in Cynoglossus zanzibarensis(Pleuronectiformes:Cynoglossidae)[J].Biochemical Systematics and Ecology,2016,66:181-187.
    [28] Wu B S,Si L Z,Kong X Y,et al.Study on feature of ITS2 in 11 Perciformes species and the application on phylogenetic relationship[J].Journal of Fishery Sciences of China,2018,25(6):1151-1160.[武宝生,司李真,孔晓瑜,等.11种鲈形目鱼类ITS2特征及系统应用[J].中国水产科学,2018,25(6):1151-1160.]
    [29] Koren S,Walenz B P,Berlin K,et al.Canu:scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation[J].Genome Research,2017,27(5):722-736.
    [30] Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheeler transform[J].Bioinformatics,2009,25(14):1754-1760.
    [31] Li H.A statistical framework for SNP calling,mutation discovery,association mapping and population genetical parameter estimation from sequencing data[J].Bioinformatics,2011,27(21):2987-2993.
    [32] Walker B J,Abeel T,Shea T,et al.Pilon:an integrated tool for comprehensive microbial variant detection and genome assembly improvement[J].PLoS One,2014,9(11):e112963.
    [33] Tamura K,Peterson D,Peterson N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.
    [34] Li Q,Wan J M.SSRHunter:development of a local searching software for SSR sites[J].Hereditas(Beijing),2005,27(5):808-810.[李强,万建民.SSRHunter,一个本地化的SSR位点搜索软件的开发[J].遗传,2005,27(5):808-810.]
    [35] Benson G.Tandem repeats finder:A program to analyze DNA sequences[J].Nucleic Acids Research,1999,27(2):573-580.
    [36] Ronquist F,Huelsenbeck J P.MrBayes 3:Bayesian phylogenetic inference under mixed models[J].Bioinformatics,2003,19(12):1572-1574.
    [37] Yang G,Yu J H,Xu P,et al.Phylogenetic relationship among 8 common species of catfish based on ribosome 18S and ITS sequences[J].Chinese Journal of Zoology,2010,45(4):110-117.[杨光,俞菊华,徐跑,等.利用18S和ITS序列揭示8种鲇形目鱼类的系统发育[J].动物学杂志,2010,45(4):110-117.]
    [38] Si L Z,Shi W,Yang M,et al.Feature analysis of the internal transcribed spacers in teleost ribosomal DNA[J].Journal of Tropical Oceanography,2016,35(6):74-81.[司李真,时伟,杨敏,等.硬骨鱼类核糖体基因间隔区的序列特征分析[J].热带海洋学报,2016,35(6):74-81.]
    [39] Galtier N,Piganeau G,Mouchiroud D,et al.GC-content evolution in mammalian genomes:The biased gene conversion hypothesis[J].Genetics,2001,159(2):907-911.
    [40] Yakovchuk P,Protozanova E,Frank-Kamenetskii M D.Base-stacking and base-pairing contributions into thermal stability of the DNA double helix[J].Nucleic Acids Research,2006,34(2):564-574.
    [41] Rodríguez-Trelles F,Tarrío R,Ayala F J.Evidence for a high ancestral GC content in Drosophila[J].Molecular Biology and Evolution,2000,17(11):1710-1717.
    [42] von der Schulenburg J H G,Hancock J M,Pagnamenta A,et al.Extreme length and length variation in the first ribosomal internal transcribed spacer of ladybird beetles(Coleoptera:Coccinellidae)[J].Molecular Biology and Evolution,2001,18(4):648-660.
    [43] Zhou A G,Xie S L,Chen J T,et al.Molecular phylogenetic relationships of five species of Epinephelus based on sequences of rDNA ITS1[J].Marine Sciences,2015,39(8):7-15.[周爱国,谢少林,陈金涛,等.5种石斑鱼核糖体DNA ITS1序列及其分子系统进化关系[J].海洋科学,2015,39(8):7-15.]
    [44] Zhang Y Z,Wang W,Jiang Z Q.Research on molecular phylogenetic relationship of partial Blennioidei based on ITS-1 sequences[J].Modern Agricultural Science and Technology,2012(8):318-320.[张源真,王伟,姜志强.基于ITS-1序列的部分鳚亚目鱼类的分子系统进化关系研究[J].现代农业科技,2012(8):318-320.]
    [45] Xu H,Li J,Kong X Y,et al.Phylogenetic relationship and length variation in the first ribosomal internal transcribed spacer of Cynoglossinae species[J].Oceanologia et Limnologia Sinica,2008,39(1):35-41.[徐晖,李军,孔晓瑜,等.6种舌鳎亚科鱼类ITS1序列长度多态性及系统分析[J].海洋与湖沼,2008,39(1):35-41.]
    [46] Gong L,Shi W,Yang M,et al.Comparative analysis of the first internal transcribed spacer of ribosomal DNA in five Soleidae species[J].Journal of Fisheries of China,2017,41(3):321-329.[龚理,时伟,杨敏,等.5种鳎科鱼类核糖体ITS1序列比较[J].水产学报,2017,41(3):321-329.]
    [47] Mu X D,Bai J J,Wang X J,et al.Cloning and sequence analysis of ribosomal DNA internal transcribed spacer 1 from goldfish(Carassius auratus)[J].Freshwater Fisheries,2008,38(1):74-76,43.[牟希东,白俊杰,汪学杰,等.金鱼核糖体转录间隔区(ITS-1)的克隆和序列分析[J].淡水渔业,2008,38(1):74-76,43.]
    [48] Yuan W A.Identification of fish species based on ribosomal DNA ITS2 locus[J].Hereditas(Beijing),2010,32(4):369-374.[袁万安.核糖体转录间隔子2应用于鱼类种属的鉴别[J].遗传,2010,32(4):369-374.]
    [49] Yang M,Kong X Y,Shi W,et al.Comparative analysis of ribosomal ITS2 sequences in 10 species of Pleuronectidae[J].Chinese Journal of Zoology,2018,53(6):938-950.[杨敏,孔晓瑜,时伟,等.鲽科10种鱼类核糖体ITS2序列比较分析[J].动物学杂志,2018,53(6):938-950.]
    [50] Schl?tterer C,Hauser M T,von Haeseler A,et al.Comparative evolutionary analysis of rDNA ITS regions in Drosophila[J].Molecular Biology and Evolution,1994,11(3):513-522.
    [51] Tang J,Toè L,Back C,et al.Intra-specific heterogeneity of the rDNA internal transcribed spacer in the Simulium damnosum(Diptera:Simuliidae)complex[J].Molecular Biology and Evolution,1996,13(1):244-252.
    [52] Fritz G N,Conn J,Cockburn A,et al.Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari(Diptera:Culicidae)[J].Molecular Biology and Evolution,1994,11(3):406-416.
    [53] Mateos M,Markow T A.Ribosomal intergenic spacer(IGS)length variation across the Drosophilinae(Diptera:Drosophilidae)[J].BMC Evolutionary Biology,2005,5:46.
    [54] Yu J H,Li H X,Ge X P,et al.Characteristics analysis of complete ribosomal DNA sequence in Chinese mitten crab(Eriocheir sinensis)[J].Journal of Fisheries of China,2010,34(5):696-703.[俞菊华,李红霞,戈贤平,等.中华绒螯蟹核糖体DNA全序列分析[J].水产学报,2010,34(5):696-703.]
    [55] Guo Z S,Ding Y,Zhang X H,et al.Complete nuclear ribosomal DNA sequence analysis of Pacific abalone Haliotis discus Hannai[J].Fisheries Science,2017,83(5):777-784.
    [56] Li L,Zhong C H,Bian Y B.The molecular diversity analysis of Auricularia auricula-judae in China by nuclear ribosomal DNA intergenic spacer[J].Electronic Journal of Biotechnology,2014,17(1):27-33.
    [57] He Y.Cloning and application of the nuclear ribosomal DNA cistron(nrDNA)sequence of two species of Pyropia in China[D].Suzhou:Soochow University,2016.[何渊.我国两种栽培紫菜核糖体RNA基因的克隆与应用[D].苏州:苏州大学,2016.]
    [58] Su X.The complete ribosome sequence amplification and characteristic analysis of five species of trematode[D].Daqing:Heilongjiang Bayi Agricultural University,2017.[宿欣.五种吸虫核糖体全序列的扩增与特征分析[D].大庆:黑龙江八一农垦大学,2017.]
    [59] Bernardi G,Olofsson B,Filipski J,et al.The mosaic genome of warm-blooded vertebrates[J].Science,1985,228(4702):953-958.
    引证文献
    网友评论
    网友评论
    分享到微博
    发 布
引用本文

杨叶欣,刘奕,刘超,宋红梅,汪学杰,牟希东.七种骨舌鱼核糖体序列特征及遗传发育分析[J].中国水产科学,2022,29(1):13-27
YANG Yexin, LIU Yi, LIU Chao, SONG Hongmei, WANG Xuejie, MU Xidong. Characteristics of ribosomal gene of seven Osteoglossidae species and molecular phylogeny[J]. Journal of Fishery Sciences of China,2022,29(1):13-27

复制
分享
文章指标
  • 点击次数:987
  • 下载次数: 1040
  • HTML阅读次数: 0
  • 引用次数: 0
历史
  • 在线发布日期: 2022-01-27
文章二维码
您是第1037521 位访问者
主管单位：中华人民共和国农业农村部
主办单位：中国水产科学研究院  中国水产学会  科学出版社
地址：北京市永定路南青塔村150号
传真：010-68673931 电话：010-68673921,010-68673931
中国水产科学 ® 2025 版权所有