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Monterrey platyfish assembly and gene annotation

Assembly

The Xiphophorus_couchianus-4.0.1 assembly was submitted by McDonnell Genome Institute - Washington University School of Medicine on November 2015. The assembly is on scaffold level, consisting of 74,316 contigs assembled into 25 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 14,608 while the scaffold N50 is 29,398,440.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001444195.1

Gene annotation

The Monterrey platyfish (Xiphophorus couchianus) is a species of freshwater fish in family Poecilidae of order Cyprinodontiformes. A live-bearer, it is native to the vicinity of Monterrey, Mexico.IUCN lists the Monterrey platyfish, formerly widespread in Mexico, as Critically Endangered, upgraded from Endangered in 1996. The fish's population, numbering fewer than 250 individuals, is falling rapidly and is confined to a very small area, occurring only in fragmented pockets of habitat populated by few individuals. It is additionally suffering from environmental degradation.X. couchianus is harvested for the aquarium fish trade. It has also been used for genetic research.Sexual dimorphism is moderate, the male Monterrey platyfish growing to a maximum overall length of 4.0 cm (1.6 in) and the female 6.0 cm (2.4 in).

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyXiphophorus_couchianus-4.0.1, INSDC Assembly GCA_001444195.1, Nov 2015
Base Pairs708,396,389
Golden Path Length708,396,389
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.401

Gene counts

Coding genes20,569
Non coding genes303
Small non coding genes288
Long non coding genes2
Misc non coding genes13
Pseudogenes38
Gene transcripts28,370

Other

Genscan gene predictions32,052

About this species