Coho salmon (Okis_V2)

Coho salmon assembly and gene annotation

Assembly

The Okis_V2 assembly was submitted by University of Victoria on November 2019. The assembly is on chromosome level, consisting of 8,771 contigs assembled into 4,087 scaffolds. From these sequences, 30 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 1,159,298 while the scaffold N50 is 68,265,700.

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.

Statistics

Summary

AssemblyOkis_V2, INSDC Assembly GCA_002021735.2, Nov 2019
Base Pairs2,375,894,934
Golden Path Length2,375,894,934
Assembly providerUniversity of Victoria
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2019
Genebuild releasedMay 2020
Genebuild last updated/patchedJan 2020
Database version111.2

Gene counts

Coding genes43,940
Non coding genes6,503
Small non coding genes3,885
Long non coding genes2,397
Misc non coding genes221
Pseudogenes561
Gene transcripts126,176

Other

Genscan gene predictions65,133