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Sailfin molly assembly and gene annotation

Assembly

The P_latipinna-1.0 assembly was submitted by The Genome Institute at Washington University School of Medicine (WUGSC) on November 2015. The assembly is on scaffold level, consisting of 54,625 contigs assembled into 17,988 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 33,278 while the scaffold N50 is 279,200.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001443285.1

Gene annotation

The sailfin molly (Poecilia latipinna) is a species of fish of the genus Poecilia. They inhabit fresh, brackish, salt, and coastal waters from North Carolina to Texas and the Yucatán Peninsula of Mexico.

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

AssemblyP_latipinna-1.0, INSDC Assembly GCA_001443285.1, Nov 2015
Base Pairs815,144,743
Golden Path Length815,144,743
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,640
Non coding genes355
Small non coding genes339
Long non coding genes2
Misc non coding genes14
Pseudogenes39
Gene transcripts32,168

Other

Genscan gene predictions46,027

About this species