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Gilthead seabream assembly and gene annotation

Assembly

The fSpaAur1.1 assembly was submitted by SC on July 2019. The assembly is on chromosome level, consisting of 1,224 contigs assembled into 176 scaffolds. From these sequences, 24 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 2,862,625 while the scaffold N50 is 35,791,275.

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

AssemblyfSpaAur1.1, INSDC Assembly GCA_900880675.1, Jul 2019
Base Pairs833,578,411
Golden Path Length833,578,411
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2019
Genebuild releasedDec 2019
Genebuild last updated/patchedSep 2019
Database version100.11

Gene counts

Coding genes25,222
Non coding genes2,273
Small non coding genes711
Long non coding genes1,542
Misc non coding genes20
Pseudogenes219
Gene transcripts73,317

Other

Genscan gene predictions54,874

About this species

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