Skip to main content
Log in

Characterization of the mitochondrial genome and phylogeny of the black arowana (Osteoglossum ferreirai)

  • Section Zoology
  • Published:
Biologia Aims and scope Submit manuscript

Abstract

In this study, we sequenced and assembled the mitochondrial (mt) genome of Osteoglossum ferreirai to re-assess the phylogenetic relationship of the family Osteoglossidae. We determined that the mitogenome of O. ferreirai contains the entire set of 37 mt genes, and the nucleotide composition and gene arrangement were similar to those of other bonytongues. Our phylogenetic analyses exhibited monophyly of the family Osteoglossidae with high bootstrap support, which is in agreement with the currently accepted phylogenetic viewpoint that is based on both morphological and molecular approaches. These findings provide additional informative data for the further study of phylogenetic relationships and help to elucidate a key component of the species radiation process within the family Osteoglossidae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Boore J.L. 1999. Animal mitochondrial genomes. Nucl. Acids Res. 27(8): 1767–1780. DOI: 10.1093/nar/27.8.1767

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Castoe T.A., de Koning A.P.J., Kim H.M., Gu W.J., Noonan B.P., Naylor G., Jiang Z.J., Parkinson C.L. & Pollock D.D. 2009. Evidence for an ancient adaptive episode of convergent molecular evolution. PNAS 106: 8986–8991. DOI: 10.1073/pnas.0900233106

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Conant G.C. & Wolfe K.H. 2008. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24(6): 861–862. DOI: 10.1093/bioinformatics/btm598

    Article  PubMed  CAS  Google Scholar 

  • Curole A.P. & Kocher T.D. 1999. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends Ecol. Evol. 14(10): 394–398. DOI: http://dx.doi.org/10.1016/S0169-5347(99)01660-2

    Article  PubMed  Google Scholar 

  • Don R.H., Cox P.T., Wainwright B.J., Baker K. & Mattick J.S. 1991. ‘Touchdown’ PCR to circumvent spurious priming during amplification. Nucl. Acids Res. 19(14): 4008. PMID: 1861999

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Duncan W.P. & Fernandes M.N. 2010. Physicochemical characterization of the white, black, and clear water rivers of the Amazon Basin and its implications on the distribution of freshwater stingrays (Chondrichthyes, Potamotrygonidae). Panamjas 5(3): 454–464.

    Google Scholar 

  • Gouy M., Guindon S. & Gascuel O. 2010. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27(2): 221–224. DOI: 10.1093/molbev/msp259

    Article  PubMed  CAS  Google Scholar 

  • Greenwood P.H., Rosen D.E., Weitzmean S.H. & Myers G.S. 1966. Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bull. Am. Mus. Nat. Hist. 131(article 4): 339–456.

    Google Scholar 

  • Hilton E.J. 2001. The tongue bite apparatus of osteoglossomorph fishes: variation of a character complex. Copeia 2001(2): 372–382. DOI: 10.1643/0045-8511(2001)001[0372:TBAOOF]2.0.CO;2

    Article  Google Scholar 

  • Hiton E.J. 2003. Comparative osteology and phylogenetic systematics of fossil and living bony-tongue fishes (Actinopterygii, Teleostei, Osteoglossomorpha). Zool. J. Linn. Soc. Lond. 137(1): 1–100. DOI: 10.1046/j.1096-3642.2003.00032.x

    Article  Google Scholar 

  • Hrbek T. & Farias IP. 2008. The complete mitochondrial genome of the pirarucu (Arapaima gigas, Arapaimidae, Osteoglossiformes). Genet. Mol. Biol. 31(1 Suppl.): 293–302. DOI: 10.1590/S1415-47572008000200024

    CAS  Google Scholar 

  • Imoto J.M., Saitoh K., Sasaki T., Yonezawa T., Adachi J., Kartavtsev Y.P., Miya M., Nishida M. & Hanzawa N. 2012. Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 514(2): 112–124. DOI: 10.1016/j.gene.2012.10.019

    Article  PubMed  Google Scholar 

  • Inoue J.G., Kumazawa Y., Miya M. & Nishida M. 2009. The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha). Mol. Phylogen. Evol. 51(3): 486–499. DOI: 10.1016/j.ympev.2009.01.020

    Article  CAS  Google Scholar 

  • Inoue J.G., Miya M., Tsukamoto K. & Nishida M. 2001. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Mol. Phylogen. Evol. 20(2): 275–285. DOI: 10.1006/mpev.2001.0970

    Article  CAS  Google Scholar 

  • Jones F.C., Grabherr M.G., Chan Y.F., et al. 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55–61. DOI: 10.1038/nature10944

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Kumazawa Y. & Mutsumi N. 2000. Molecular phylogeny of Osteoglossoids: a new model for Gondwanian origin and Plate Tectonic transportation of the Asian arowana. Mol. Biol. Evol. 17(12): 1869–1878. PMID: 11110903

    Article  PubMed  CAS  Google Scholar 

  • Lavoué S. & Sullivan J. 2004. Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha: Teleostei). Mol. Phylogen. Evol. 33(1): 171–185 DOI: 10.1016/j.ympev.2004.04.021

    Article  Google Scholar 

  • Lavoué S., Miya M., Arnegard M.E., McIntyre P.B., Mamonekene V. & Nishida M. 2011. Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence. Proc. R. Soc. B 278: 1003–1008. DOI: 10.1098/rspb.2010.1639

    Article  PubMed  PubMed Central  Google Scholar 

  • Lavoué S., Miya M., Arnegard M.E., Sullivan J.P., Hopkins C.D. & Nishida M. 2012. Comparable ages for the independent origins of Electrogenesis in African and South American weakly electric fishes. PLoS ONE 7: e36287. DOI: 10.1371/journal.pone.0036287

    Article  PubMed  PubMed Central  Google Scholar 

  • Li G.Q. & Wilson M.V.H., 1996. Phylogeny of Osteoglossomorpha, Chapter 8, pp. 163–174. DOI: 10.1016/B978-012670950-6/50009-6. In: Stiassny, M.L.J., Parenti, L.R., Johnson, G.D. (eds), Interrelationships of Fishes, Academic Press, New York, 496 pp. ISBN: 978-0-12-670950-6

    Google Scholar 

  • Li J.T., Li Y., Klaus S., Rao D.Q. Hillis D.M. & Zhang Y.P. 2013a. Diversification of rhacophorid frogs provides evidence for accelerated faunal exchange between India and Eurasia during the Oligocene. PNAS 110: 3441–3446. DOI: 10.1073/pnas.1300881110

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Li Y.L., Ren Z.M., Shedlock A.M., Wu J.Q., Sang L., Tersing T.S., Hasegawa M., Yonezawa T. & Zhong Y. 2013b. High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses. Gene 517(2): 169–178. DOI: 10.1016/j.gene.2012.12.096.

    Article  PubMed  CAS  Google Scholar 

  • Mabuchi K., Miya M., Senou H., Suzuki T. & Nishida M. 2006. Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): further evidence for an ancient origin. Aquaculture 257(1–4): 68–77. DOI: 10.1016/j.aquaculture.2006.03.040

    Article  CAS  Google Scholar 

  • McGuire J.A., Linkem C.W., Koo M.S., Hutchison D.W., Lappin A.K., Orange D.I., Lemos-Espinal J., Riddle B.R. & Jaeger J.R. 2007. Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution 61(12): 2879–2897. DOI: 10.1111/j.1558-5646.2007.00239.x

    Article  PubMed  CAS  Google Scholar 

  • Mohd-Shamsudin M.I., Fard M.Z., Mather P.B., Suleiman Z., Hassan R., Othman R.Y. & Bhassu S. 2011. Molecular characterization of relatedness among colour variants of Asian arowana (Scleropages formosus). Gene 490(1–2): 47–53. DOI: 10.1016/j.gene.2011.08.025.

    Article  PubMed  CAS  Google Scholar 

  • Mu X.D., Hu Y.C., Wang X.J., Song H.M., Yang Y.X. & Luo J.R. 2011. Genetic variability in cultured stocks of Scleropages formosus in mainland China revealed by microsatellite markers. J. Anim. Vet. Adv. 10(5): 555–561. DOI: 10.3923/javaa.2011.555.561

    Article  CAS  Google Scholar 

  • Mu X.D., Wang X.J., Song H.M., Yang Y.X., Luo D., Gu D.E., Xu M., Liu C. Luo J.R. & Hu Y.C. 2012. Mitochondrial DNA as effective molecular markers for the genetic variation and phylogeny of the family Osteoglossidae. Gene 511(2): 320–325 DOI: 10.1016/j.gene.2012.09.087

    Article  PubMed  CAS  Google Scholar 

  • Murphy W.J. & Collier G.E. 1996. Phylogenetic relationships within the aplocheiloid fish genus Rivulus (Cyprinodontiformes, Rivulidae): implications for Caribbean and Central American biogeography. Mol. Biol. Evol. 13(5): 642–649. DOI: 10.35).06/1996; 13(5):642-9.

    Article  PubMed  CAS  Google Scholar 

  • Nakatani M., Miya M., Mabuchi K., Saitoh K. & Nishida M. 2011. Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evol. Biol. 11: 177. DOI: 10.1186/1471-2148-11-177

    Article  PubMed  PubMed Central  Google Scholar 

  • Nelson J.S. 2006. Fishes of the World, fourth ed. John Wiley and Sons, Inc., New York, 624 pp. ISBN: 0-471-25031-7, 978-0-471-25031-9

    Google Scholar 

  • Ojala D., Merkel C., Gelfand R. & Attardi G. 1980. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 22(2 Pt 2): 393–403. DOI: 10.1016/0092-8674(80)90350-5

    Article  PubMed  CAS  Google Scholar 

  • Olivares A.M, Hrbek T., Escobar M.D. & Caballero S. 2013. Population structure of the black arowana (Osteoglossum ferreirai) in Brazil and Colombia: implications for its management. Conserv. Genet. 14(2): 695–703. DOI: 10.1007/s10592-013-0463-1

    Article  Google Scholar 

  • Rasmussen A.S. & Rnason U.A. 1999. Molecular studies suggest that cartilaginous fishes have a terminal position in the piscine tree. PNAS 96(5): 2177–2182. PMID: 26756

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Ronquist F. 1997. Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Syst. Biol. 46(1): 195–203. DOI: 10.1093/sysbio/46.1.195

    Article  Google Scholar 

  • Ronquist F. & Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12): 1572–1574. DOI: 10.1093/bioinformatics/btg180

    Article  PubMed  CAS  Google Scholar 

  • Ruber L., Britz R., Tan H.H., Ng P.K.L. & Zardoya R. 2004. Evolution of mouth brooding and life-history correlates in the fighting fish genus Betta. Evolution 58(4): 799–813. DOI: http://dx.doi.org/10.1554/03-364

    Article  PubMed  Google Scholar 

  • Saitoh K., Sado T., Doosyey M., Bart Jr. H., Inoue J., Nishida M., Mayden R. & Miya M. 2011. Evidene from mitochondrial genomics supports the lower Mesozoci of South Asia as the time and place of basal divergence of Cypriniform fishes (Actinopterygii: Ostariophysi). Zool. J. Linn. Soc. 161(3): 633–662. DOI: 10.1111/j.1096-3642.2010.00651.x

    Article  Google Scholar 

  • Saitoh K., Sado T., Mayden R.L., Hanzawa N., Nakamura K., Nishida M. & Miya M. 2006. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The first evidence toward resolution of higher-level relationships of the World’s largest freshwater fish clade based on 59 whole mitogenome sequences. J. Mol. Evol. 63(6): 826–841. DOI: 10.1007/s00239-005-0293-y

    Article  PubMed  CAS  Google Scholar 

  • Swofford D.L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts. http://www.sinauer.com/paupphylogenetic-analysis-using-parsimony-and-other-methods-4-0-beta.html

    Google Scholar 

  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M. & Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28(10): 2731–2739. DOI: 10.1093/molbev/msr121

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F. & Higgins D.G. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25(24): 4876–4882. PMID: 9396791

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Wang X.T., Zhang Y.F., Wu Q. & Zhang H. 2012. Evolutionary landscape of amphibians emerging from ancient freshwater fish inferred from complete mitochondrial genomes. Biochem. Biophys. Res. Commun. 421(2): 228–231. DOI: 10.1016/j.bbrc.2012.03.141

    Article  PubMed  CAS  Google Scholar 

  • Wilson M.V.H. & Murray A.M. 2008. Osteoglossomorpha: phylogeny, biogeography, and fossil record and the significance of key African and Chinese fossil taxa. Geol. Soc. Lond. Spec. Publ. 295: 185–219. DOI: 10.1144/SP295.12

    Article  Google Scholar 

  • Wyman S.K., Jansen R.K. & Boore J.L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics Applications Note 20(17): 3252–3255. DOI: 10.1093/bioinformatics/bth352

    Article  CAS  Google Scholar 

  • Yu L., Wang X., Ting N. & Zhang Y. 2011. Mitogenomic analysis of Chinese snub-nosed monkeys: evidence of positive selection in NADH dehydrogenase genes in highaltitude adaptation. Mitochondrion 11(3): 497–503. DOI: 10.1016/j.mito.2011.01.004

    Article  PubMed  CAS  Google Scholar 

  • Yue G.H., Li Y., Lim L.C. & Orban L. 2004. Monitoring the genetic diversity of three Asian arowana (Scleropages formosus) stocks using AFLP and microsatellites. Aquaculture 237(1–4): 89–102. DOI: 10.1016/j.aquaculture.2004.04.003

    Article  CAS  Google Scholar 

  • Yue G.H., Liew W.C. & Orban L. 2006.The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae). BMC Genomics 7: 242. DOI: 10.1186/1471-2164-7-242

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jianren Luo.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mu, X., Liu, Y., Wang, X. et al. Characterization of the mitochondrial genome and phylogeny of the black arowana (Osteoglossum ferreirai). Biologia 69, 1222–1230 (2014). https://doi.org/10.2478/s11756-014-0426-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.2478/s11756-014-0426-0

Key words

Navigation