Platyfish assembly and gene annotation


Platyfish are members of the Poeciliidae family. The genus Xiphophorus is composed of 27 described species of both platyfish and swordtails that are found from northeastern Mexico (Coahuila) as far south as Honduras (2200 km). The Xiphophorus maculatus fish utilized for genome sequencing was a female of the 104th inbred generation from the X. maculatus/Jp 163 A, a line maintained at The Xiphophorus Genetic Stock Center. This release features the first preliminary assembly of the X. maculatus/Jp 163 A genome, XipMac4.4.2, provided by The Genome Institute, Washington University School of Medicine. This whole genome shotgun assembly was produced from two independent assemblies built with all sequence data, using the Newbler and PCAP algorithms from ~19.6X total sequence coverage. A merged assembly was achieved using graph accordance. The genome assembly displayed here comprises 20,640 scaffolds with an N50 of 1.3 Mb. These scaffolds have been assembled from a set of 67,070 contigs with an N50 of 22.3 kb. The final ungapped sequence length is 653 Mb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000241075.1

Gene annotation

XipMac4.4.2 was annotated using the Ensembl genebuild pipeline. Gene models are based on

  • Genewise alignments of UniProt protein sequences from platyfish
  • Models build from platyfish RNASeq data using our in-house RNASeq pipeline
  • Genewise alignments of UniProt protein sequences from other fish and vertebrate species
  • Exonerate alignments of Ensembl Stickleback and Zebrafish proteins from Ensembl release 65

Protein-coding models were extended into their untranslated regions using RNASeq models. In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated.

More information

General information about this species can be found in Wikipedia.



AssemblyXipmac4.4.2, INSDC Assembly GCA_000241075.1, Jan 2012
Base Pairs652,830,449
Golden Path Length729,679,499
Annotation methodFull genebuild
Genebuild startedJan 2012
Genebuild releasedSep 2012
Genebuild last updated/patchedApr 2013
Database version93.1

Gene counts

Coding genes20,379
Gene transcripts20,854


Genscan gene predictions71,811

About this species