title: X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species.
abstract: BACKGROUND
  Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species.
  
  
  RESULTS
  We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus.
  
  
  CONCLUSIONS
  Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.
authors.affiliation: The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA. shenyj@xmu.edu.cn.|Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, A316 Environment and Ecology Bldg., Xiamen, Fujian, 361102, China. shenyj@xmu.edu.cn.
authors.forename: Yingjia
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France. domitille.chalopin@ens-lyon.fr.
authors.forename: Domitille
authors.initials: D
authors.lastname: Chalopin
authors.affiliation: The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA. tzintzuni@gmail.com.
authors.forename: Tzintzuni
authors.initials: T
authors.lastname: Garcia
authors.affiliation: The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA. mboswell@txstate.edu.
authors.forename: Mikki
authors.initials: M
authors.lastname: Boswell
authors.affiliation: The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA. wb1016@txstate.edu.
authors.forename: William
authors.initials: W
authors.lastname: Boswell
authors.affiliation: The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA. shiryaev@ncbi.nlm.nih.gov.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Shiryev
authors.affiliation: The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA. richa@helix.nih.gov.
authors.forename: Richa
authors.initials: R
authors.lastname: Agarwala
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France. Jean-Nicolas.Volff@ens-lyon.fr.
authors.forename: Jean-Nicolas
authors.initials: JN
authors.lastname: Volff
authors.affiliation: Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, OR, 97403, USA. jpostle@uoneuro.uoregon.edu.
authors.forename: John H
authors.initials: JH
authors.lastname: Postlethwait
authors.affiliation: Universität Würzburg, Physiologische Chemie I, Biozentrum, Am Hubland, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany. phch1@biozentrum.uni-wuerzburg.de.
authors.forename: Manfred
authors.initials: M
authors.lastname: Schartl
authors.affiliation: Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA. pminx@genome.wustl.edu.
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.affiliation: Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA. wwarren@genome.wustl.edu.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.affiliation: The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA. RWalter@txstate.edu.
authors.forename: Ronald B
authors.initials: RB
authors.lastname: Walter
mesh_terms: D000818:Animals; D003532:Cyprinodontiformes / Q000235:genetics*; D005786:Gene Expression Regulation; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*