The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

Nature Genetics

Volumn 45, Issue 5, 2013, Pages 567-572

  Schartl, Manfred ^a,b   Walter, Ronald B ^c   Shen, Yingjia ^c   Garcia, Tzintzuni ^c   Catchen, Julian ^d   Amores, Angel ^d   Braasch, Ingo ^a,d   Chalopin, Domitille ^e   Volff, Jean Nicolas ^e   Lesch, Klaus Peter ^b   Bisazza, Angelo ^f   Minx, Pat ^g   Hillier, Ladeana ^g   Wilson, Richard K ^g   Fuerstenberg, Susan ^h   Boore, Jeffrey ^h   Searle, Steve ⁱ   Postlethwait, John H ^d   Warren, Wesley C ^g  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b UNIVERSITY HOSPITAL WÜRZBURG   (Germany)

^c Texas State University   (United States)

^d UNIVERSITY OF OREGON   (United States)

^e UNIVERSITÉ LYON 1   (France)

^f UNIVERSITY OF PADOVA   (Italy)

^g WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h Genome Project Solutions   (United States)

ⁱ EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME ANALYSIS; DUPLICATE GENE; EVOLUTIONARY ADAPTATION; FISH; GENE MAPPING; GENE SEQUENCE; GENETIC TRAIT; GENOME; MOLECULAR BIOLOGY; NONHUMAN; PRIORITY JOURNAL; VIVIPARITY; XIPHOPHORUS MACULATUS;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BIOLOGICAL EVOLUTION; CYPRINODONTIFORMES; FEMALE; FISH PROTEINS; GENE DUPLICATION; GENOME; MEIOSIS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SELECTION, GENETIC; SEX CHROMOSOMES; SYNTENY; VIVIPARITY, NONMAMMALIAN;

AMPHIBIA; MAMMALIA; REPTILIA; TELEOSTEI; VERTEBRATA; XIPHOPHORUS MACULATUS;

EID: 84878607707     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2604     Document Type: Article

References (58)

1. Volff, J.N., Bouneau, L., Ozouf-Costaz, C. & Fischer, C. Diversity of retrotransposable elements in compact pufferfish genomes. Trends Genet. 19, 674-678 (2003).
2. Gifford, R. & Tristem, M. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26, 291-315 (2003).
3. Katzourakis, A., Gifford, R.J., Tristem, M., Gilbert, M.T. & Pybus, O.G. Macroevolution of complex retroviruses. Science 325, 1512 (2009).
4. Han, G.Z. & Worobey, M. An endogenous foamy virus in the Aye-Aye (Daubentonia madagascariensis). J. Virol. 86, 7696-7698 (2012).
5. Han, G.Z. & Worobey, M. An endogenous foamy-like viral element in the coelacanth genome. PLoS Pathog. 8, e1002790 (2012).
6. Llorens, C., Munoz-Pomer, A., Bernad, L., Botella, H. & Moya, A. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees. Biol. Direct 4, 41 (2009).
7. Ferguson-Smith, M.A. & Trifonov, V. Mammalian karyotype evolution. Nat. Rev. Genet. 8, 950-962 (2007).
8. Amores, A., Catchen, J., Ferrara, A., Fontenot, Q. & Postlethwait, J.H. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics 188, 799-808 (2011).
9. Walter, R.B. et al. A microsatellite genetic linkage map for Xiphophorus. Genetics 168, 363-372 (2004).
10. Catchen, J.M., Conery, J.S. & Postlethwait, J.H. Automated identification of conserved synteny after whole-genome duplication. Genome Res. 19, 1497-1505 (2009).
11. Miya, M. et al. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26, 121-138 (2003).
12. Steinke, D., Salzburger, W. & Meyer, A. Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J. Mol. Evol. 62, 772-784 (2006).
13. Patton, E.E., Mitchell, D.L. & Nairn, R.S. Genetic and environmental melanoma models in fish. Pigment Cell and Melanoma Res. 23, 314-337 (2010).
14. Wittbrodt, J. et al. Novel putative receptor tyrosine kinase encoded by the melanoma-inducing Tu locus in Xiphophorus. Nature 341, 415-421 (1989).
15. Kallman, K.D. The platyfish Xiphophorus maculatus. in Handbook of Genetics Vol. 4 (ed. King, R.C.) 81-132 (Plenum Press, New York, 1975).
16. Gutbrod, H. & Schartl, M. Intragenic sex-chromosomal crossovers of Xmrk oncogene alleles affect pigment pattern formation and the severity of melanoma in Xiphophorus. Genetics 151, 773-783 (1999).
17. Meierjohann, S. & Schartl, M. From Mendelian to molecular genetics: the Xiphophorus melanoma model. Trends Genet. 22, 654-661 (2006).
18. Braasch, I., Brunet, F., Volff, J.N. & Schartl, M. Pigmentation pathway evolution after whole-genome duplication in fish. Genome Biol. Evol. 1, 479-493 (2009).
19. Laisney, J.A., Mueller, T.D., Schartl, M. & Meierjohann, S. Hyperactivation of constitutively dimerized oncogenic EGF receptors by autocrine loops. Oncogene published online; doi:10.1038/onc.2012.267 (2 July 2012).
20. Regneri, J. & Schartl, M. Expression regulation triggers oncogenicity of xmrk alleles in the Xiphophorus melanoma system. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 155, 71-80 (2012).
21. Kazianis, S. et al. Localization of a CDKN2 gene in linkage group V of Xiphophorus fishes defines it as a candidate for the DIFF tumor suppressor. Genes Chromosom. Cancer 22, 210-220 (1998).
22. Chatzinasiou, F. et al. Comprehensive field synopsis and systematic meta-analyses of genetic association studies in cutaneous melanoma. J. Natl. Cancer Inst. 103, 1227-1235 (2011).
23. Butler, A.P. et al. Regulation of CDKN2A/B and Retinoblastoma genes in Xiphophorus melanoma. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 145, 145-155 (2007).
24. Walter, R.B. & Kazianis, S. Xiphophorus interspecies hybrids as genetic models of induced neoplasia. ILAR J. 42, 299-321 (2001).
25. Nairn, R.S. et al. Genetic analysis of susceptibility to spontaneous and UV-induced carcinogenesis in Xiphophorus hybrid fish. Mar. Biotechnol. (NY) 3, S24-S36 (2001).
26. Kazianis, S. et al. Genetic analysis of neoplasia induced by N-nitroso-N-methylurea in Xiphophorus hybrid fish. Mar. Biotechnol. (NY) 3, S37-S43 (2001).
27. Hrbek, T., Seckinger, J. & Meyer, A. A phylogenetic and biogeographic perspective on the evolution of poeciliid fishes. Mol. Phylogenet. Evol. 43, 986-998 (2007).
28. Pollux, B.J.A., Pires, M.N., Banet, A.I. & Reznick, D.N. Evolution of placentas in the fish family Poeciliidae: an empirical study of macroevolution. Annu. Rev. Ecol. Evol. Syst. 40, 271-289 (2009).
29. Turner, C.L. Pseudoamnion, pseudochorion, and follicular pseudoplacenta in poeciliid fishes. J. Morphol. 67, 59-87 (1940).
30. Tavolga, W.N. & Rugh, R. Development of the platyfish, Platypoecilius maculatus. Zoologica 32, 1-15 (1947).
31. Scrimshaw, N.S. Embryonic development in poeciliid fishes. Biol. Bull. 88, 233-246 (1945).
32. Brawand, D., Wahli, W. & Kaessmann, H. Loss of egg yolk genes in mammals and the origin of lactation and placentation. PLoS Biol. 6, e63 (2008).
33. Sibley, C.P. et al. Placental-specific insulin-like growth factor 2 (Igf2) regulates the diffusional exchange characteristics of the mouse placenta. Proc. Natl. Acad. Sci. USA 101, 8204-8208 (2004).
34. Vo, L.H. & Hedrick, J.L. Independent and hetero-oligomeric-dependent sperm binding to egg envelope glycoprotein ZPC in Xenopus laevis. Biol. Reprod. 62, 766-774 (2000).
35. Bshary, R., Wickler, W. & Fricke, H. Fish cognition: a primate's eye view. Anim. Cogn. 5, 1-13 (2002).
36. Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545 (1999).
37. Braasch, I. & Postlethwait, J.H. Fish polyploidy and the teleost genome duplication. in Polyploidy and Genome Evolution (eds. Soltis, P.S. & Soltis, D.E.) 341-383 (Springer, Berlin, Heidelberg, 2012).
38. Galtier, N., Gouy, M. & Gautier, C. SEAVIEW and PHYLO-WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12, 543-548 (1996).
39. Setiamarga, D.H. et al. Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates. Biol. Lett. 5, 812-816 (2009).
40. Froschauer, A. et al. Construction and initial analysis of bacterial artificial chromosome (BAC) contigs from the sex-determining region of the platyfish Xiphophorus maculatus. Gene 295, 247-254 (2002).
41. Huang, X., Wang, J., Aluru, S., Yang, S.P. & Hillier, L. PCAP: a whole-genome assembly program. Genome Res. 13, 2164-2170 (2003).
42. Yao, G. et al. Graph accordance of next-generation sequence assemblies. Bioinformatics 28, 13-16 (2012).
43. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
44. Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
45. Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19 (suppl. 2), ii215-ii225 (2003).
46. Kent, W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
47. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
48. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
49. Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
50. Schulz, M.H., Zerbino, D.R., Vingron, M. & Birney, E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086-1092 (2012).
51. Wu, T.D. & Watanabe, C.K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859-1875 (2005).
52. Lowe, T.M. & Eddy, S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
53. Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973-982 (2007).
54. Kohany, O., Gentles, A.J., Hankus, L. & Jurka, J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7, 474 (2006).
55. Xu, Z. & Wang, H. LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265-W268 (2007).
56. Catchen, J.M., Amores, A., Hohenlohe, P., Cresko, W. & Postlethwait, J.H. Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda) 1, 171-182 (2011).
57. Hohenlohe, P.A. et al. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet. 6, e1000862 (2010).
58. Yang, Z., Wong, W.S. & Nielsen, R. Bayes empirical bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22, 1107-1118 (2005).