Ensembl mobile site help

Things to know when navigating the Ensembl mobile site

Search box

Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more.

Top navigation

Touch MENU button to open the main menu and touch again to close.

Touch MENU

Left hand side menu

Touch the left menu icon () or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close.

The ? icon

Touch the icon to get help

And don't forget to send us your comments using the feedback link inside the main menu.

EnsemblEnsembl Home

Western mosquitofish assembly and gene annotation

Assembly

The ASM309773v1 assembly was submitted by University of Georgia on May 2018. The assembly is on scaffold level, consisting of 73,682 contigs assembled into 2,943 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 17,511 while the scaffold N50 is 6,651,460.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_003097735.1

Gene annotation

The western mosquitofish (Gambusia affinis) is a species of freshwater fish, also known commonly, if ambiguously, as simply mosquitofish or by its generic name, Gambusia, or by the common name gambezi. There is also an eastern mosquitofish (G. holbrooki).Mosquitofish are small in comparison to many other freshwater fish, with females reaching an overall length of 7 cm (2.8 in) and males at a length of 4 cm (1.6 in). The female can be distinguished from the male by her larger size and a gravid spot at the posterior of her abdomen. The name "mosquitofish" was given because the diet of this fish sometimes consists of large numbers of mosquito larvae, relative to body size. Gambusia typically eat zooplankton, beetles, mayflies, caddisflies, mites, and other invertebrates; mosquito larvae make up only a small portion of their diet.Mosquitofish were introduced directly into ecosystems in many parts of the world as a biocontrol to lower mosquito populations which in turn negatively affected many other species in each distinct bioregion. Mosquitofish in Australia are classified as a noxious pest and may have exacerbated the mosquito problem in many areas by outcompeting native invertebrate predators of mosquito larvae. Several counties in California distribute mosquitofish at no charge to residents with manmade fish ponds and pools as part of their mosquito abatement programs. The fish are made available to residents only and are intended to be used solely on their own property, not introduced into natural habitat. On 24 February 2014, Chennai Corporation in India introduced western mosquitofish in 660 ponds to control the mosquito population in freshwater bodies.Fertilization is internal; the male secretes milt into the genital aperture of the female through his gonopodium. Within 16 to 28 days after mating, the female gives birth to about 60 young. The males reach sexual maturity within 43 to 62 days. The females, if born early in the reproductive season, reach sexual maturity within 21 to 28 days; females born later in the season reach sexual maturity in six to seven months.

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

AssemblyASM309773v1, INSDC Assembly GCA_003097735.1, May 2018
Base Pairs598,663,367
Golden Path Length598,663,367
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes21,724
Non coding genes306
Small non coding genes292
Long non coding genes2
Misc non coding genes12
Pseudogenes27
Gene transcripts33,089

Other

Genscan gene predictions34,937

About this species