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

• Published in: Nature genetics Vol. 45; no. 5; pp. 567 - 572
• Main Authors: Schartl, Manfred, Walter, Ronald B, Shen, Yingjia, Garcia, Tzintzuni, Catchen, Julian, Amores, Angel, Braasch, Ingo, Chalopin, Domitille, Volff, Jean-Nicolas, Lesch, Klaus-Peter, Bisazza, Angelo, Minx, Pat, Hillier, LaDeana, Wilson, Richard K, Fuerstenberg, Susan, Boore, Jeffrey, Searle, Steve, Postlethwait, John H, Warren, Wesley C
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.05.2013; Nature Publishing Group
• Subjects: 631/1647/2217; 631/208/182; 631/208/212; Adaptation, Physiological - genetics; Agriculture; American Recovery & Reinvestment Act 2009-US; Amphibians; Animal Genetics and Genomics; Animals; Biological Evolution; Biomedicine; Cancer Research; Chromosomes; Computer Science; Cyprinodontiformes - genetics; DNA sequencing; Ecological adaptation; Female; Fish Proteins - genetics; Freshwater; Gene Duplication; Gene Function; Genetics; Genome; Genomes; Genomics; Human Genetics; letter; Life Sciences; Mammals; Meiosis - genetics; Melanoma; Methods; Molecular biology; Molecular Sequence Data; Nucleotide sequencing; Phylogeny; Reptiles; Selection, Genetic; Sex Chromosomes - genetics; Software packages; Synteny; Teleostei; Viruses; Viviparity, Nonmammalian; Xiphophorus maculatus; Germany; DE-NOVO; DNA-SEQUENCES; GENETIC-ANALYSIS; MELANOMA; ALIGNMENT; RNA-SEQ; POECILIID FISHES; DUPLICATION; PROGRAM; HYBRID FISH
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.2604

Wesley Warren and colleagues report the whole-genome sequence of the platyfish, Xiphophorus maculatus , providing the first genome of a poeciliid fish. They provide a resource for this model organism used to study traits including viviparity, complex behaviors, pigmentation and cancer, and their comparative analysis provides insights into evolutionary adaptations in natural teleost populations. Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus , offers a unique model to better understand the molecular biology of such traits. We report here the sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps identified an unexpected evolutionary stability of chromosomes in fish, in contrast to in mammals. Genes associated with viviparity show signatures of positive selection, identifying new putative functional domains and rare cases of parallel evolution. We also find that genes implicated in cognition show an unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles.