Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications

Molecular Biology Reports

Volumn 38, Issue 3, 2011, Pages 2015-2021

  He, Anyuan ^a   Luo, Yongju ^b   Yang, Hong ^c   Liu, Liping ^a   Li, Sifa ^a   Wang, Chenghui ^a  

^a SHANGHAI OCEAN UNIVERSITY   (China)

^b Guanxi Fisheries Institute   (China)

^c SOUTH CHINA SEA FISHERIES RESEARCH INSTITUTE   (China)

Author keywords

Cichlidae; Mitochondrial DNA; Oreochromis aureus; Oreochromis niloticus; Phylogeny

Indexed keywords

MITOCHONDRIAL DNA; MITOCHONDRIAL PROTEIN; RIBOSOME RNA; TRANSFER RNA;

ANIMAL CELL; ARTICLE; DNA SEQUENCE; GENE NUMBER; GENETIC ASSOCIATION; GENETIC ORGANIZATION; GENOME ANALYSIS; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; OREOCHROMIS AUREUS; OREOCHROMIS NILOTICUS; PARSIMONY ANALYSIS; PHYLOGENY;

ANIMALS; BASE SEQUENCE; DNA, INTERGENIC; DNA, MITOCHONDRIAL; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PHYLOGENY; RNA, RIBOSOMAL; RNA, TRANSFER; TILAPIA;

CICHLIDAE; OREOCHROMIS; OREOCHROMIS AUREUS; OREOCHROMIS MOSSAMBICUS; OREOCHROMIS NILOTICUS; PISCES;

EID: 79951578414     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-010-0324-7     Document Type: Article

References (42)

1. Nelson JS (2006) Fishes of the world, 4th edn. Wiley, New York, pp 390
2. V Klett A Meyer 2002 What, if anything, is a Tilapia?-mitochondrial ND2 phylogeny of tilapiines and the evolution of parental care systems in the African cichlid fishes Mol Biol Evol 19 865 883 1:CAS:528:DC%2BD38Xks1Ojtb0%3D 12032243 (Pubitemid 34602957)
3. TD Kocher 2004 Adaptive evolution and explosive speciation: the cichlid fish model Nat Rev Genet 5 288 298 1:CAS:528:DC%2BD2cXjtVartLs%3D 10.1038/nrg1316 15131652 (Pubitemid 38435624)
4. S Kuraku A Meyer 2008 Genomic analysis of cichlid fish 'natural mutants' Curr Opin Genet Dev 18 551 558 1:CAS:528:DC%2BD1MXhtFCjsr0%3D 10.1016/j.gde.2008.11.002 19095433
5. W Salzburger A Meyer 2004 The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics Naturwissenschaften 91 277 290 1:CAS:528:DC%2BD2cXlsVCrsr0%3D 10.1007/s00114-004-0528-6 15241604 (Pubitemid 38916482)
6. O Seehausen 2006 African cichlid fish: a model system in adaptive radiation research Proc Biol Sci 273 1987 1998 10.1098/rspb.2006.3539 16846905 (Pubitemid 44214911)
7. GF Turner 2007 Adaptive radiation of cichlid fish Curr Biol 17 R827 R831 1:CAS:528:DC%2BD2sXhtFCjtL3L 10.1016/j.cub.2007.07.026 17925206 (Pubitemid 47503788)
8. E Trewavas 1981 Addendum to Tilapia and Sarotherodon? Buntbarsche Bull 87 12
9. E Trewavas 1982 Genetic groupings of Tilapiini used in aquaculture Aquaculture 27 79 81 10.1016/0044-8486(82)90112-0 (Pubitemid 15274409)
10. Trewavas E (1983) Tilapiine fishes of the genera Sarotherodon, Oreochromis, and Danakilia. British Museum (Natural History), London, p 583
11. MRR Romana-Eguia M Ikeda ZU Basiao N Taniguchi 2004 Genetic diversity in farmed Asian Nile and red hybrid tilapia stocks evaluated from microsatellite and mitochondrial DNA analysis Aquaculture 236 131 150 1:CAS:528: DC%2BD2cXktVCis7c%3D 10.1016/j.aquaculture.2004.01.026 (Pubitemid 38629960)
12. HL Khaw RW Ponzoni MJC Danting 2008 Estimation of genetic change in the GIFT strain of Nile tilapia (Oreochromis niloticus) by comparing contemporary progeny produced by males born in 1991 or in 2003 Aquaculture 275 64 69 10.1016/j.aquaculture.2008.01.022
13. G Liao 2000 The distribution of Tilapias Fishery Abroad 38 38 41
14. P Chakrabarty 2006 Systematics and historical biogeography of Greater Antillean Cichlidae Mol Phylogenet Evol 39 619 627 10.1016/j.ympev.2006.01.014 16495088
15. KR Dinesh TM Lim WK Chan VPE Phang 1996 Genetic variation inferred from RAPD fingerprinting in three species of tilapia Aquacult Int 4 19 30 10.1007/BF00175218
16. JP Franck I Kornfield JM Wright 1994 The utility of SATA satellite DNA sequences for inferring phylogenetic relationships among the three major genera of tilapiine cichlid fishes Mol Phylogenet Evol 3 10 16 1:CAS:528: DyaK2MXht1Whuw%3D%3D 10.1006/mpev.1994.1002 7545936
17. SJ Lee CC Ju SL Chu MS Chien TH Chan WL Liao 2007 Molecular cloning, expression and phylogenetic analyses of parvalbumin in tilapia, Oreochromis mossambicus J Exp Zool A Ecol Genet Physiol 307 51 61 10.1002/jez.a.345 17094115 (Pubitemid 46333554)
18. K Mabuchi M Miya Y Azuma M Nishida 2007 Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes BMC Evol Biol 7 10 10.1186/1471-2148-7-10 17263894
19. Z Musilova O Rican K Janko J Novak 2008 Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae) Mol Phylogenet Evol 46 659 672 1:CAS:528: DC%2BD1cXhvF2gt70%3D 10.1016/j.ympev.2007.10.011 18055225 (Pubitemid 351215926)
20. GAC Pérez O Iíban G Ortí E Bermingham I Doadrio R Zardoya 2007 Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene Mol Phylogenet Evol 43 91 110 10.1016/j.ympev.2006.08.012 17045493 (Pubitemid 46505272)
21. O Rican R Zardoya I Doadrio 2008 Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology Mol Phylogenet Evol 49 941 957 1:CAS:528: DC%2BD1cXhsVCntLzF 10.1016/j.ympev.2008.07.022 18725305
22. S Nagl H Tichy WE Mayer IE Samonte BJ McAndrew J Klein 2001 Classification and phylogenetic relationships of African tilapiine fishes inferred from mitochondrial DNA sequences Mol Phylogenet Evol 20 361 374 1:CAS:528:DC%2BD3MXmtleis7o%3D 10.1006/mpev.2001.0979 11527464 (Pubitemid 32835884)
23. YP Kartavtsev S-O Jung Y-M Lee H-K Byeon J-S Lee 2007 Complete mitochondrial genome of the bullhead torrent catfish, Liobagrus obesus (Siluriformes, Amblycipididae): Genome description and phylogenetic considerations inferred from the Cyt b and 16S rRNA genes Gene 1 13 27 10.1016/j.gene.2007.01.027 (Pubitemid 46818776)
24. P Kosa M Valach L Tomaska KH Wolfe J Nosek 2006 Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants Nucleic Acids Res 34 2472 2481 1:CAS:528:DC%2BD28Xks1Sls78%3D 10.1093/nar/gkl327 16684995 (Pubitemid 43985685)
25. G Lin L Lo ZY Zhu F Feng R Chou GH Yue 2006 The complete mitochondrial genome sequence and characterization of single-nucleotide polymorphisms in the control region of the Asian seabass (Lates calcarifer) Mar Biotechnol 8 71 79 1:CAS:528:DC%2BD28XhsFCktb0%3D 10.1007/s10126-005-5051-z 16228120 (Pubitemid 43273258)
26. Z Peng J Wang S He 2006 The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes Gene 376 290 297 1:CAS:528:DC%2BD28XmsVGlsrc%3D 10.1016/j.gene.2006.04.014 16737786
27. K Saitoh K Hayashizaki Y Yokoyama T Asahida H Toyohara Y Yamashita 2000 Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships J Hered 91 271 278 1:CAS:528:DC%2BD3cXlsV2mu7c%3D 10.1093/jhered/91.4.271 10912672 (Pubitemid 30457453)
28. C Wang Q Chen G Lu J Xu Q Yang S Li 2008 Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): insight into its phylogenic position within Cyprinidae Gene 424 96 101 1:CAS:528: DC%2BD1cXhtF2ms7jL 10.1016/j.gene.2008.07.011 18706492
29. X Wu L Wang S Chen R Zan H Xiao YP Zhang 2010 The complete mitochondrial genomes of two species from Sinocyclocheilus (Cypriniformes: Cyprinidae) and a phylogenetic analysis within Cyprininae Mol Biol Rep 37 2163 2171 1:CAS:528:DC%2BC3cXotVWkurs%3D 10.1007/s11033-009-9689-x 19688279
30. GH Yue WC Liew L Orban 2006 The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae) BMC Genomics 7 242 10.1186/1471-2164-7-242 16989663 (Pubitemid 44509392)
31. X Zhang B Yue W Jiang Z Song 2009 The complete mitochondrial genome of rock carp Procypris rabaudi (Cypriniformes: Cyprinidae) and phylogenetic implications Mol Biol Rep 36 981 991 1:CAS:528:DC%2BD1MXjvFaqu78%3D 10.1007/s11033-008-9271-y 18496768
32. Sambrook J, Russell DW (2002) Molecular cloning: a laboratory manual, 3rd edn. pp 461-471
33. M Miya H Takeshima H Endo NB Ishiguro JG Inoue T Mukai TP Satoh M Yamaguchi A Kawaguchi K Mabuchi SM Shirai M Nishida 2003 Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences Mol Phylogenet Evol 26 121 138 1:CAS:528: DC%2BD38Xps1WhtL4%3D 10.1016/S1055-7903(02)00332-9 12470944 (Pubitemid 36029259)
34. Hall T (2005) BioEdit v7.0.5 http://www.mbio.ncsu.edu/BioEdit/page2.html
35. D Ojala C Merkel R Gelfand G Attardi 1980 The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA Cell 22 393 403 1:CAS:528:DyaL3MXkt1yhtg%3D%3D 10.1016/0092-8674(80)90350-5 7448867 (Pubitemid 11199897)
36. Lowe TM, Eddy SR (1997) tRNAscan-SE 1.21 http://lowelab.ucsc.edu/ tRNAscan-SE/
37. RC Edgar 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 32 1792 1797 1:CAS:528:DC%2BD2cXisF2ks7w%3D 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
38. Jobb (2008) TREEFINDER version of February 2007. Munich (Germany)
39. Swofford DL (2003) PAUP*: phylogenetic analysis using parsimony (and other methods). version 4.0b10. Sinauer Associates, Sunderland, MA
40. F Ronquist JP Huelsenbeck 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 1574 1:CAS:528:DC%2BD3sXntlKms7k%3D 10.1093/bioinformatics/btg180 12912839 (Pubitemid 37038874)
41. D Posada TR Buckley 2004 Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests Syst Biol 53 793 808 10.1080/ 10635150490522304 15545256 (Pubitemid 39568279)
42. WJ Lee J Conroy WH Howell TD Kocher 1995 Structure and evolution of teleost mitochondrial control regions J Mol Evol 41 54 66 1:CAS:528: DyaK2MXmt1yktrw%3D 10.1007/BF00174041 7608989