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Shortfin molly assembly and gene annotation

Poecilia mexicana, commonly known as the shortfin molly or Atlantic molly, is a species of poeciliid fish native to fresh and brackish water in Mexico and Guatemala. One population is found in caves and known as the cave molly.


The P_mexicana-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 50,601 contigs assembled into 18,105 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 39,840 while the scaffold N50 is 275,316.

Gene annotation

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.



AssemblyP_mexicana-1.0, INSDC Assembly GCA_001443325.1, Nov 2015
Base Pairs801,711,499
Golden Path Length801,711,499
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version104.1

Gene counts

Coding genes24,074
Non coding genes359
Small non coding genes343
Long non coding genes2
Misc non coding genes14
Gene transcripts35,365


Genscan gene predictions46,082

About this species