Atlantic salmon (Ssal_v3.1)

Atlantic salmon assembly and gene annotation

Assembly

The Ssal_v3.1 assembly was submitted by Norwegian University Of Life Sciences on April 2021. The assembly is on chromosome level, consisting of 4,222 contigs assembled into 4,222 scaffolds. From these sequences, 29 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 28,058,890 while the scaffold N50 is 28,058,890.

Other assemblies

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

AssemblySsal_v3.1, INSDC Assembly GCA_905237065.2, Apr 2021
Base Pairs2,756,584,103
Golden Path Length2,756,584,103
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2021
Genebuild released
Genebuild last updated/patchedJul 2021
Database version111.31

Gene counts

Coding genes47,205
Non coding genes21,576
Small non coding genes8,669
Long non coding genes12,851
Misc non coding genes56
Pseudogenes608
Gene transcripts184,209

Other

Genscan gene predictions70,362