ZHENG Lianming, HE Jinru, LIN Yuanshao, CAO Wenqing, ZHANG Wenjing. 16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China[J]. Acta Oceanologica Sinica, 2014, 33(4): 55-76. doi: 10.1007/s13131-014-0415-8
Citation: ZHENG Lianming, HE Jinru, LIN Yuanshao, CAO Wenqing, ZHANG Wenjing. 16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China[J]. Acta Oceanologica Sinica, 2014, 33(4): 55-76. doi: 10.1007/s13131-014-0415-8

16S rRNA is a better choice than COI for DNA barcoding hydrozoans in the coastal waters of China

doi: 10.1007/s13131-014-0415-8
  • Received Date: 2013-06-17
  • Rev Recd Date: 2013-10-20
  • Identification of hydrozoan species is challenging, even for taxonomic experts, due to the scarcity of distinct morphological characters and phenotypic plasticity. DNA barcoding provides an efficient method for species identification, however, the choice between mitochondrial cytochrome c oxidase subunit Ⅰ (COI) and large subunit ribosomal RNA gene (16S) as a standard barcode for hydrozoans is subject to debate. Herein, we directly compared the barcode potential of COI and 16S in hydrozoans using 339 sequences from 47 pelagic hydrozoan species. Analysis of Kimura 2-parameter genetic distances (K2P) documented the mean intraspecific/interspecific variation for COI and 16S to be 0.004/0.204 and 0.003/0.223, respectively. An obvious "barcoding gap" was detected for all species in both markers and all individuals of a species clustered together in both the COI and 16S trees. These results suggested that the species within the studied taxa can be efficiently and accurately identified by COI and 16S. Furthermore, our results confirmed that 16S was a better phylogenetic marker for hydrozoans at the genus level, and in some cases at the family level. Considering the resolution and effectiveness for barcoding and phylogenetic analyses of Hydrozoa, we strongly recommend 16S as the standard barcode for hydrozoans.
  • loading
  • Bouillon J, Boero F. 2000. The Hydrozoa: A new classification in thelight of old knowledge. Thalassia Salentina, 24: 1-45
    Bridge D, Cunningham C W, DeSalle R, et al. 1995. Class-level relationshipsin the Phylum Cnidaria: molecular and morphological evidence.Molecular Biology and Evolution, 12: 679-689
    Bucklin A, Ortman B D, Jennings R M, et al. 2010. A "Rosetta Stone" forzooplankton: DNA barcode analysis of holozooplankton diversityof the Sargasso Sea (NW Atlantic Ocean). Deep-Sea Research Ⅱ, 57: 2234-2247
    Bucklin A, Steinke D, Blanco-Bercial L. 2011. DNA barcoding of marinemetazoa. Annual Review of Marine Science, 3: 471-508
    Cantero A L P, Sentandreu V, Latorre A. 2010. Phylogenetic relationshipsof the endemic Antarctic benthic hydroids (Cnidaria, Hydrozoa):what does the mitochondrial 16S rRNA tell us about it? Polar Biology,33: 41-57
    Cartwright P, Evans N M, Dunn C W, et al. 2008. Phylogenetics of Hydroidolina(Hydrozoa: Cnidaria). Journal of the Marine BiologicalAssociation of the United Kingdom, 88: 1663-1672
    Collins A G. 2000. Towards understanding the phylogenetic history of Hydrozoa: hypothesis testing with 18S gene sequence data. ScientiaMarina, 64: 5-22
    Collins A G. 2002. Phylogeny of Medusozoa and the evolution of cnidarianlife cycles. Journal of Evolutionary Biology, 15: 418-432
    Collins A G, Bentlage B, Lindner A, et al. 2008. Phylogenetics of Trachylina(Cnidaria: Hydrozoa) with new insights on the evolution ofsome problematic taxa. Journal of the Marine Biological Associationof the United Kingdom, 88: 1673-1685
    Collins A G, Schuchert P, Marques A C, et al. 2006. Medusozoan phylogenyand character evolution clarified by new large and smallsubunit rDNA data and an assessment of the utility of phylogeneticmixture models. Systematic Biology, 55: 97-115
    Collins A G, Winkelmann S, Hadrys H, et al. 2005. Phylogeny of Capitataand Corynidae (Cnidaria, Hydrozoa) in light of mitochondrial16S rDNA data. Zoologica Scripta, 34: 91-99
    del-Prado R, Cubas P, Lumbsch H T, et al. 2010. Genetic distances withinand among species in monophyletic lineages of Parmeliceae(Ascomycota) as a tool for taxon delimitation. Molecular Phylogeneticsand Evolution, 56: 125-133
    Dawson M N. 2003. Macro-morphological variation mong cryptic specieof the moon jellyfish, Aurelia (Cnidaria: Scyphozoa). MarineBiology, 143: 369-379
    Dawson M N. 2005. Cyanea capillata is not a cosmopolitan jellyfish:morphological and molecular evidence for C. annaskala and C.rosea (Scyphozoa: Semaeostomeae: Cyaneidae) in south-easternAustralia. Invertebrate Systematics, 19: 361-370
    Dawson M N, Jacobs D K. 2001. Molecular evidence for cryptic speciesof Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin, 200:92-96
    Dawson M N, Martin L E. 2001. Geographic variation and ecologicaladaptation in Aurelia (Scyphozoa, Semaeostomeae): some implicationsfrom molecular phylogenetics. Hydrobiologia, 451:259-273
    Dunn C W, Pugh P R, Haddock S H D. 2005. Molecular phylogenetics ofthe siphonophora (Cnidaria), with implications for the evolutionof functional specialization. Systematic Biology, 54: 916-935
    Ender A, Schierwater B. 2003. Placozoa are not derived cnidarians: evidencefrom molecular morphology. Molecuar Biology Evolution,20: 130-134
    Faith D P, Williams K J. 2005. How large-scale DNA barcoding programscan boost biodiversity conservation planning: linking phylogeneticdiversity (PD) analyses to the barcode of life database(BoLD). Abstract. In: Australian entomological society's 36thAGM and scientific conference/7th invertebrate biodiversityand conservation conference/Australian systematics society,Canberra, Australia, 4-9 December 2005
    Folino-Rorem N C, Darling J A, D'Ausilio C A. 2008. Genetic analysisreveals multiple cryptic invasive species of the hydrozoan genusCordylophora. Biological Invasions, 11: 1869-1882
    Folmer O, Black M, Hoeh W, et al. 1994. DNA primers for amplificationof mitochondrial cytochrome c oxidase subunit I from diversemetazoan invertebrates. Molecular Marine Biology and Biotechnology,3: 294-299
    Govindarajan A F, Boero F, Halanych K M. 2006. Phylogenetic analysiswith multiple markers indicates repeated loss of the adult medusastage in Campanulariidae (Hydrozoa, Cnidaria). MolecularPhylogenetics and Evolution, 38: 820-834
    Govindarajan A F, Halanych K M, Cunningham C W. 2005a. Mitochondrialevolution and phylogeography in the hydrozoan Obelia geniculata(Cnidaria). Marine Biology, 146: 213-222
    Govindarajan A F, Piraino S, Gravili C, et al. 2005b. Species identificationof bivalve-inhabiting marine hydrozoans of the genus Eugymnanthea.Invertebrate Biology, 124: 1-10
    Hajibabaei M, Janzen D H, Burns J M, et al. 2006. DNA barcodes distinguishspecies of tropical Lepidoptera. Proceedings of the NationalAcademy of Sciences of the United States of America, 103:968-971
    Hajibabaei M, Singer G A C, Hebert P D N, et al. 2007. DNA barcoding:how it complements taxonomy, molecular phylogenetics andpopulation genetics. Trends in Genetics, 23: 167-172
    Hebert P D N, Gregory T R. 2005. The promise of DNA barcoding fortaxonomy. Systematic Biology, 54: 852-859
    Hebert P D N, Penton E H, Burns J M, et al. 2004a. Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipperbutterfly Astraptes fulgerator. Proceedings of the National Academyof Science of the United States of America, 101: 14812-14817
    Hebert P D N, Ratnasingham S, deWaard J R. 2003. Barcoding animallife: cytochrome c oxidase subunit I divergences among closelyrelated species. Proceedings of the Royal Society B-BiologicalSciences, 270: S96-S99
    Hebert P D N, Stoeckle M Y, Zemlak T S, et al. 2004b. Identification ofbirds through DNA barcodes. PloS Biology, 2: 1657-1663
    Hellberg M E. 2006. No variation and low synonymous substitutionrates in coral mtDNA despite high nuclear variation. BMC EvolutionaryBiology, 6: 1-8
    Holland B S, Dawson M N, Crow G L, et al. 2004. Global phylogeographyof Cassiopea (Scyphozoa: Rhizostomeae): molecular evidencefor cryptic species and multiple invasions of the HawaiianIslands. Marine Biology, 145: 1119-1128
    Huang D, Meier R, Todd P A, et al. 2008. Slow mitochondrial COI sequenceevolution at the base of the metazoan tree and its implicationsfor DNA barcoding. Journal of Molecular Evolution, 66:167-174
    Kimura M. 1980. A simple method for estimating evolutionary rates ofbase substitutions through comparative studies of nucleotidesequences. Journal of Molecular Evolution, 16: 111-120
    Köhler F. 2007. From DNA taxonomy to barcoding: how a vague ideaevolved into a biosystematic tool. Mitteilungen aus dem Museumfür Naturkunde Berlin Zoologische Reihe, 83: 44-51
    Krishnamurthy P K, Francis R A. 2012. A critical review on the utilityof DNA barcoding in biodiversity conservation. Biodiversity andConservation, 21: 1901-1919
    Kubota S. 1983. Studies on life history and systematics of the Japanesecommensal hydroids living in bivalves, with some reference totheir evolution. Journal of the Faculty of Science Hokkaido UniversitySeries VI Zoology, 23: 296-402
    Kubota S. 2000. Parallel, paedomorphic evolutionary processes of thebivalve-inhabiting hydrozoans (Leptomedusae, Eirenidae) deducedfrom morphology, life cycle and biogeography, with specialreference to taxonomic treatment of Eugymnanthea. ScientiaMarina, 64: 241-247
    Larkin M A, Blackshields G, Brown N P, et al. 2007. Clustal W and clustalX version 2.0. Bioinformatics, 23: 2947-2948
    Leclère L, Schuchert P, Cruaud C, et al. 2009. Molecular phylogeneticsof Thecata (Hydrozoa, Cnidaria) reveals long-term maintenanceof life history traits despite high frequency of recent characterchanges. Systematic Biology, 58: 509-526
    Leclère L, Schuchert P, Manuel M. 2007. Phylogeny of the Plumularioidea(Hydrozoa, Leptothecata): evolution of colonial organizationand life cycle. Zoologica Scripta, 36: 371-394
    Le Goff-Vitry M C, Rogers A D, Baglo牷椠湄攮?椲漰氰漴朮椠捁愠汤??獰猠潳捥楡愠瑳楬潡湮?漠景?琠桴敨?啭湯楬瑥散摵??楲渠杰摨潹浬???????て???????leractinia. Molecular Phylogeneticsand Evolution, 30: 167-177
    Martinez D E, Iniguez A R, Percell K M, et al. 2010. Phylogeny and biogeographyof Hydra (Cnidaria: Hydridae) using mitochondrialand nuclear DNA sequences. Molecular Phylogenetics and Evolution,57: 403-410
    McFadden C S, Benayahu Y, Pante E, et al. 2011. Limitations of mitochondrialgene barcoding in Octocorallia. Molecular EcologyResources, 11: 19-31
    McFadden C S, Tullis I, Hutchinson M B, et al. 2000. Rates of evolutionof cnidarian mitochondrial genes. American Zoologist, 40:1124-1124
    Meyer C P, Paulay G. 2005. DNA barcoding: error rates based on comprehensivesampling. PLoS Biolog, 3: 2229-2238
    Miglietta M P, Piraino S, Kubota S, et al. 2007. Species in the genus Turritopsis(Cnidaria, Hydrozoa): a molecular evaluation. Journal ofZoological Systematics and Evolutionary Research, 45: 11-19
    Miglietta M P, Schuchert P, Cunningham C W. 2009. Reconciling genealogicaland morphological species in a worldwide study of theFamily Hydractiniidae (Cnidaria, Hydrozoa). Zoologica Scripta,38: 403-430
    Mills C E. 1995. Medusae, siphonophores, and ctenophores as planktivorouspredators in changing global ecosystems. ICES Journalof Marine Science, 52: 575-581
    Miranda L S, Collins A G, Marques A C. 2010. Molecules clarify a Cnidarianlife cycle—the “Hydrozoan” Microhydrula limopsicola isan early life stage of the Staurozoan Haliclystus antarcticus. PLoSOne, 5: e10182
    Moritz C, Cicero C. 2004. DNA barcoding: promise and pitfalls. Plos Biology,2: 1529-1531
    Moura C J, Cunha M R, Porteiro F M, et al. 2011a. Polyphyly and crypticdiversity in the hydrozoan families Lafoeidae and Hebellidae(Cnidaria:Hydrozoa). Invertebrate Systematics, 25: 454-470
    Moura C J, Cunha M R, Porteiro F M, et al. 2011b. The use of the DNAbarcode gene 16S mRNA for the clarification of taxonomicproblems within the family Sertulariidae (Cnidaria, Hydrozoa).Zoologica Scripta, 40: 520-537
    Moura C J, Cunha M R, Porteiro F M, et al. 2012. A molecular phylogeneticappraisal of the systematics of the Aglaopheniidae (Cnidaria:Hydrozoa, Leptothecata) from the north-east Atlantic andwest Mediterranean. Zoological Journal of the Linnean Society,164: 717-727
    Moura C J, Harris D J, Cunha M R, et al. 2008. DNA barcoding revealscryptic diversity in marine hydroids (Cnidaria, Hydrozoa) fromcoastal and deep-sea environments. Zoologica Scripta, 37: 93-108
    Nawrocki A M, Schuchert P, Cartwright P. 2010. Phylogenetics and evolutionof Capitata (Cnidaria: Hydrozoa), and the status of thefamily Corynidae. Zoological Scripta, 39: 290-304
    Ortman B D, Bucklin A, Pagès F, et al. 2010. DNA barcoding the Medusozoausing mtCOI. Deep-Sea Research II: Topical Studies inOceanography, 57: 2148-2156
    Pontin D R, Cruickshank R H. 2012. Molecular phylogenetics of the genusPhysalia (Cnidaria: Siphonophora) in New Zealand coastalwaters reveals cryptic diversity. Hydrobiologia, 686: 91-105
    Ratnasingham S, Hebert P D N. 2007. BOLD: the barcode of life datasystem (http://www.barcodinglife.org). Molecular EcologyNotes, 7: 355-364
    Schuchert P. 2005a. Species boundaries in the hydrozoan genus Coryne.Molecular Phylogenetics and Evolution, 36: 194-199
    Schuchert P. 2005b. Rediscovery of Coryne fucicola (de Filippi, 1866)(Cnidaria: Hydrozoa). Cahiers de Biologie Marine, 46: 305-310
    Schuchert P. 2006. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Capitata Part 1. Revue Suisse de Zoologie,113: 325-410
    Schuchert P. 2007. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 2. Revue Suisse de Zoologie,114: 195-396
    Schuchert P. 2008a. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 3. Revue Suisse de Zoologie,115: 221-302
    Schuchert P. 2008b. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 4. Revue Suisse de Zoologie,115: 677-757
    Schuchert P. 2009. The European athecate hydroids and their medusae(Hydrozoa, Cnidaria): Filifera Part 5. Revue Suisse de Zoologie,116: 441-507
    Schuchert P, Reiswig H M. 2006. Brinckmannia hexactinellidophila,n.genera, n. sp. a hydroid living in tissues of glass sponges of thereefs, fjords, and seamounts of Pacific Canada and Alaska. CanadianJournal of Zoology, 84: 564-572
    Shearer T L, van Oppen M J H, Romano S L, et al. 2002. Slow mitochondrialDNA sequence evolution in the Anthozoa (Cnidaria). MolecularEcology, 11: 2475-2487
    Sinniger F, Reimer J D, Pawlowski J. 2008. Potential of DNA sequencesto identify zoanthids (Cnidaria: Zoantharia). Zoological Science,25: 1253-1260
    Stampar S N, Maronna M M, Vermeij M J A, et al. 2012. Evolutionarydiversification of banded tube-dwelling anemones (Cnidaria;Ceriantharia; Isarachnanthus) in the Atlantic Ocean. PLoS One,7: e41091
    Sun Yan, Li Qi, Kong Lingfeng, et al. 2012. DNA barcoding of Caenogastropodaalong coast of China based on the COI gene. MolecularEcology Resources, 12: 209-218
    Tamura K, Peterson D, Peterson N, et al. 2011. MEGA5: Molecular evolutionarygenetics analysis using maximum likelihood, evolutionarydistance, and maximum parsimony methods. MolecularBiology and Evolution, 28: 2731-2739
    Ward R D, Zemlak T S, Innes B H, et al. 2005. DNA barcoding Australia'sfish species. Philosophical Transactions of the Royal Society B—Biological Sciences, 360: 1847-1857
    Xia Yun, Gu Haifeng, Peng Rui, et al. 2012. COI is better than 16S rRNAfor DNA barcoding Asiatic salamanders (Amphibia: Caudata:Hynobiidae). Molecular Ecology Resources, 12: 48-56
    Zemlak T S, Ward R D, Connell A D, et al. 2009. DNA barcoding revealsoverlooked marine fishes. Molecular Ecology Resources, 9: 237-242
    Zheng Lianming, Lin Yuanshao, Li Shaojing, et al. 2009. Aequorea taiwanensisn. sp (Hydrozoa, Leptomedusae) and mtCOI sequenceanalysis for the genus Aequorea. Acta Oceanologica Sinica, 28:109-115
    Zhou Konglin, Zheng Lianming, He Jinru, et al. 2013. Detection of anew Clytia species (Cnidaria: Hydrozoa: Campanulariidae) withDNA barcoding and life cycle analyses. Journal of the Ma
  • 加载中


    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Article Metrics

    Article views (1918) PDF downloads(3648) Cited by()
    Proportional views


    DownLoad:  Full-Size Img  PowerPoint