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Turbot assembly and gene annotation

Assembly

The ASM318616v1 assembly was submitted by CNAG on June 2018. The assembly is on chromosome level, consisting of 21,326 contigs assembled into 22 scaffolds. From these sequences, 22 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 54,836 while the scaffold N50 is 24,811,384.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_003186165.1

Gene annotation

The turbot (Scophthalmus maximus) is a species of flatfish in the family Scophthalmidae. It is a demersal fish native to marine or brackish waters of the North Atlantic, Baltic Sea and the Mediterranean Sea.

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

AssemblyASM318616v1, INSDC Assembly GCA_003186165.1, Jun 2018
Base Pairs524,979,463
Golden Path Length524,979,463
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJun 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes21,000
Non coding genes420
Small non coding genes401
Long non coding genes2
Misc non coding genes17
Pseudogenes27
Gene transcripts35,543

Other

Genscan gene predictions32,205

About this species