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    Xiphophorus Genome Project, in collaboration with
Texas State University San Marcos and University of Wurzburg
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The Xiphophorus maculatus Genome Project

The genus Xiphophorus comprises 27 recognized species of live-bearing fishes that populate freshwater habitats in the slopes of the Sierra Madre uplifts of Mexico, and extending into Guatemala, Belize, and Honduras. In native habitats, combinations of spatial, ecological, behavioral, and anatomic factors discourage cross-species mating, such that naturally occurring interspecific Xiphophorus hybrids are virtually unknown. In the laboratory, however, most members of the genus are inter-fertile with one another and produce fertile offspring. Experimental crossing of many different species have revealed a diversity of developmental perturbations influencing the regulation of pigmentation patterns and intensity, growth and maturation rates, behavioral patterns, alternative sex determination mechanisms, and susceptibilities to spontaneous or induced neoplasias. Consequently, the Xiphophorus species genetic system represents an easily manipulated and astoundingly diverse model system for examining the evolution of interacting gene complexes and for dissecting the genetic bases of developmental programs, behaviors, and the molecular processes underlying neoplastic initiation and progression.

The X. maculatus genome sequence is derived from a single highly inbred (104th generation) adult female fish from the Xiphophorus Genetic Stock Center. This genome sequence enables comparisons of gene content and structure implicated in the regulation of complex traits identified in interspecific hybrid crosses. In addition, the availability of Xiphophorus sequence will allow investigators to take advantage of the extensive genomic resources of the pufferfish (Fugu rubripes), zebrafish (Danio rerio), and medaka (Oryzias latipes) to predict the genomic structures and identification of factors associated with interesting complex traits, thereby facilitating the discovery of candidate genes for further study.

The genomes listed below have been analyzed by the PHRINGE ("Phylogenetic Resources for the Interpretation of Genomes") pipeline. Briefly described, PHRINGE creates a graph with all inferred protein sequences as nodes, with edges formed from distance scores calculated from their full length alignments, then clusters these into gene families using a method that considers the evolutionary relationships among the organisms, then performs a phylogenetic analysis on each. This allows the most accurate possible assignment of orthologous and paralogous relationships, inference of retained gene function, and reconstruction of gene duplications and losses. Users can see the multiple sequence alignments and phylogenetic trees of all genes, compare intron-exon structures, and see the relative arrangements of homologs across all genomes. See a summary of the PHRINGE method, details of the PHRINGE pipeline, or an explanation of why it is important to use evolutionary analysis to find orthologs.

This project is being led by Professor Ronald Walter of Texas State University San Marcos and Manfred Schartl of the University of Wurzburg . Credit for informatics work and database design and construction goes to Bob Stiles of Roundtrip Networks, Wayne Huang of Linear Time, and Asoke Talukder of Geschickten.

Genomes Currently Being Presented
Organism Details Group
Sequenced by Genome URL Publication
Strongylocentrotus purpuratus 1 Echinodermata
BCM Project Home Sondergren et al., Science 2006 Nov 10; 314(5801):941-52
Ciona intestinalis 2 Urochordata
JGI Assembly Dehal et al., Science 13 December 2002: Vol. 298 no. 5601 pp. 2157-2167
Xiphophorus maculatus 3 Teleosts
WUGSC Project Home In preperation
Oryzias latipes 4 Teleosts
NIG and University of Tokyo Assembly Unpublished
Gastersteus aculatus 5 Teleosts
Broad Assembly Kingsley, D. M. (2003).
Tetraodon nigroviridis 6 Teleosts
Genoscope Genome Browser Roest Crollius H. et al. Genome Res. (2000) 10, 939-949.
Danio rerio 7 Teleosts
Sanger Assembly Broughton RE et al.,Genome Res, 2001 Nov; 11(11):1958-67
Xenopus tropicalis 8 Amphibia
JGI Browser Gateway Hellsten, U, et al., Science, 2010; 328 (5978): 633-636
Gallus gallus 9 Aves
WUGSC Assembly Chicken Genome Consortium Nature 432: 695-716
Monodelphis domestica 10 Mammalia
Broad Browser Gateway Mikkelsen, TS, et al.,Nature 447, 167-177
Mus musculus 11 Mammalia
Mouse Genome Sequencing Consortium (MGSC) Assembly Chinwalla, A.T. et al., Nature 420, 520-562
Homo sapiens 12 Mammalia
The Genome Reference Consortium Browser Gateway International Human Genome Sequencing Consortium. Nature. 2004 Oct 21;431(7011):931-45.
For the Detail Page of a particular gene, enter one of these identifiers
PHRINGE Gene or Protein ID
Maximum distance to show
Maximum matches per taxon to show
"Detail Pages" contain information on a particular gene, including its position, length, and intron-exon structure, most similar sequences with links, and the clusters (at various phylogenetic depths) to which it has been assigned by PHRINGE. Find a Detail Page either by the query above or by clicking on any particular gene box on a Synteny Page. The cluster ID is linked to the corresponding "Cluster and Compare Page".

"Cluster and Compare Pages" contain information on a particular PHRINGE cluster, including the multiple sequence alignment, comparison of intron-exon structures, and the phylogeny of the member genes. Find a Cluster and Compare Page from the cluster IDs on a corresponding Detail Page.

"Synteny Pages" show an overview of the relative physical arrangements of homologous genes for specified portions of specified genomes. Connecting lines are red if there has been an inversion. Mouse over gene boxes for more information.


For the Synteny Page of relative gene arrangements
Query genome
Scaffold (or chromosome) #
First gene position #
Last gene position #
Max Gene Distance
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(to maximize the portions in the same orientation)
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Genomes to compare Ciona intestinalis
Danio rerio
Gallus gallus
Gastersteus aculatus
Homo sapiens
Monodelphis domestica
Mus musculus
Oryzias latipes
Tetraodon nigroviridis
Xenopus tropicalis
Xiphophorus maculatus