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.
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Boore J.L. 1999. Animal mitochondrial genomes. Nucl. Acids Res. 27(8): 1767–1780. DOI: 10.1093/nar/27.8.1767
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
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
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
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
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.
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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.
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
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
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.
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
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
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.
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
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
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
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
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
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
Ronquist F. & Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12): 1572–1574. DOI: 10.1093/bioinformatics/btg180
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
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
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
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
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
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
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
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
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
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
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
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
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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
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DOI: https://doi.org/10.2478/s11756-014-0426-0