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Greater amberjack assembly and gene annotation

Assembly

The Sdu_1.0 assembly was submitted by Genomic breeding group, Research Center for Aquatic Breeding, National Research Institute of aquaculture, FRA on August 2017. The assembly is on scaffold level, consisting of 41,188 contigs assembled into 34,656 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 249,509 while the scaffold N50 is 5,812,906.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_002260705.1

Gene annotation

The greater amberjack (Seriola dumerili) is a jack of the genus Seriola. It is found in the Mediterranean Sea, the Atlantic Ocean, the Pacific Ocean and the Indian coasts, living usually between 20 and 70 m of depth (with a maximum of 360 m). It is the largest genus in the family Carangidae, with a maximum length of 200 cm. It is a fast-swimming pelagic fish with similar habits to the kingfish. They are silver-blue with a golden side line, with a brown band crossing over the eye area.The greater amberjack is a powerful hunter which feeds on other fish and invertebrates.The greater amberjack is prized by sport fisherman because it is a very powerful fish and can be quite large, even as much as 70 kg. It is an excellent eating fish. It is also a big-game fish and are one of the greatest fighting fish pound for pound.

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

AssemblySdu_1.0, INSDC Assembly GCA_002260705.1, Aug 2017
Base Pairs677,686,174
Golden Path Length677,686,174
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,278
Non coding genes526
Small non coding genes504
Long non coding genes2
Misc non coding genes20
Pseudogenes41
Gene transcripts33,754

Other

Genscan gene predictions37,425

About this species