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

Manfred Schartl (1, 2) , Ronald B. Walter (3) , Yingjia Shen (3) , Tzintzuni Garcia (3) , Julian Catchen (4) , Angel Amores (4) , Ingo Braasch (4, 1) , Domitille Chalopin (5) , Jean-Nicolas J.-N. Volff (5) , Klaus-Peter Lesch (6) , Angelo Bisazza (7) , Pat Minx (8) , Ladeana Hillier (8) , Richard K. Wilson (8) , Susan Fuerstenberg (9) , Jeffrey Boore (9) , Steve Searle (10) , John H. Postlethwait (4) , Wesley C. Warren (8)

1 University of Würzburg
2 University Clinic Würzburg
3 Department of Chemistry and Biochemistry
4 Institute of Neuroscience
5 IGFL - Institut de Génomique Fonctionnelle de Lyon
6 University Hospital of Würzburg
7 Unipd - Università degli Studi di Padova = University of Padua
8 The Genome Institute
9 Genome Project Solutions
10 Wellcome Trust

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.

Mots clés: RNA-SEQ; DE-NOVO; POECILIID FISHES; GENETIC-ANALYSIS; DNA-SEQUENCES; HYBRID FISH; ALIGNMENT; PROGRAM

Mots clés: MELANOMA; DUPLICATION

Domaines: Sciences du Vivant [q-bio]; Informatique [cs]

Manfred Schartl, Ronald B. Walter, Yingjia Shen, Tzintzuni Garcia, Julian Catchen, et al.. The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics, 2013, 45 (5), pp.567-U150. ⟨10.1038/ng.2604⟩. ⟨hal-02648822⟩