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Atlantic salmon assembly and gene annotation

Assembly

The ICSASG_v2 assembly was submitted by International Cooperation to Sequence the Atlantic Salmon Genome on June 2015. The assembly is on chromosome level, consisting of 368,060 contigs assembled into 241,573 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 57,618 while the scaffold N50 is 1,366,254.

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

AssemblyICSASG_v2, INSDC Assembly GCA_000233375.4, Jun 2015
Base Pairs3,412,130,248
Golden Path Length3,412,130,248
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2019
Genebuild releasedDec 2019
Genebuild last updated/patchedDec 2019
Database version100.2

Gene counts

Coding genes47,329
Non coding genes7,650
Small non coding genes4,988
Long non coding genes2,501
Misc non coding genes161
Pseudogenes840
Gene transcripts130,585

Other

Genscan gene predictions197,403

About this species

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