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Platyfish assembly and gene annotation

Assembly

The X_maculatus-5.0-male assembly was submitted by The Genome Institute, Washington University at St. Louis on December 2017. The assembly is on chromosome level, consisting of 258 contigs assembled into 102 scaffolds. From these sequences, 24 chromosomes have been built. 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 9,181,372 while the scaffold N50 is 31,535,491.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_002775205.2

Gene annotation

The southern platyfish, common platy, or moonfish (Xiphophorus maculatus) is a species of freshwater fish in family Poeciliidae of order Cyprinodontiformes. A live-bearer, it is closely related to the green swordtail (X. hellerii) and can interbreed with it. It is native to an area of North and Central America stretching from Veracruz, Mexico, to northern Belize.The southern platyfish grows to a maximum overall length of 6.0 centimetres (2.4 in). Sexual dimorphism is slight, the male’s caudal fin being more pointed. The anal fin of the male fish has evolved into a gonopodium, a stick-shaped organ used for reproduction. The female southern platyfish's anal fin is fan shaped. Wild varieties are drab in coloration, lacking the distinctive dark lateral line common to many Xiphophorus species.X. maculatus prefers slow-moving waters of canals, ditches, and warm springs. Omnivorous, its diet includes both plants and small crustaceans, insects, and annelid worms.Breeders have developed a multitude of color varieties (e.g. orange, red, yellow, red/black, and black/white) which are common aquarium fish for hobbyists.The southern platyfish is commonly known simply as the platy (pl. platys or platies), from the fish’s original generic name, Platypoecilus.

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

AssemblyX_maculatus-5.0-male, INSDC Assembly GCA_002775205.2, Dec 2017
Base Pairs704,321,165
Golden Path Length704,321,165
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.5

Gene counts

Coding genes23,774
Non coding genes397
Small non coding genes377
Long non coding genes2
Misc non coding genes18
Pseudogenes38
Gene transcripts37,048

Other

Genscan gene predictions40,494

About this species