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Sheepshead minnow assembly and gene annotation

Assembly

The C_variegatus-1.0 assembly was submitted by Aquatic Genome Models on July 2014. The assembly is on scaffold level, consisting of 110,959 contigs assembled into 9,259 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 20,803 while the scaffold N50 is 835,301.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000732505.1

Gene annotation

The sheepshead minnow or sheepshead pupfish (Cyprinodon variegatus variegatus) is a subspecies of ray-finned fish in the family Cyprinodontidae, the pupfishes. It is found in salt marsh and estuary environments and is native to the eastern coasts of North and Central America.

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

AssemblyC_variegatus-1.0, INSDC Assembly GCA_000732505.1, Oct 2015
Base Pairs1,035,184,475
Golden Path Length1,035,184,475
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,019
Non coding genes404
Small non coding genes387
Long non coding genes4
Misc non coding genes13
Pseudogenes35
Gene transcripts33,363

Other

Genscan gene predictions46,874

About this species