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Yellowtail amberjack assembly and gene annotation

Seriola lalandi dorsalis, the yellowtail amberjack, is a species of ray-finned fish of the family Carangidae, found in the Southern Ocean. It has been established as a suitable candidate for marine aquaculture, with juveniles being produced in hatcheries from captive breeding stock.

Assembly

The Sedor1 assembly was submitted by Iowa State University on December 2017. The assembly is on scaffold level, consisting of 133,262 contigs assembled into 99,598 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 51,346 while the scaffold N50 is 1,269,737.

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

AssemblySedor1, INSDC Assembly GCA_002814215.1, Dec 2017
Base Pairs732,509,836
Golden Path Length732,509,836
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedMar 2020
Database version100.1

Gene counts

Coding genes24,755
Non coding genes865
Small non coding genes839
Long non coding genes2
Misc non coding genes24
Pseudogenes67
Gene transcripts34,514

Other

Genscan gene predictions56,220

About this species

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