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Turbot assembly and 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.

Assembly

The ASM1334776v1 assembly was submitted by CIGENE on June 2020. The assembly is on chromosome level, consisting of 178 contigs assembled into 127 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 20,466,349 while the scaffold N50 is 25,949,660.

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

AssemblyASM1334776v1, INSDC Assembly GCA_013347765.1, Jun 2020
Base Pairs556,696,898
Golden Path Length556,696,898
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2020
Genebuild releasedMar 2021
Genebuild last updated/patchedDec 2020
Database version104.1

Gene counts

Coding genes21,263
Non coding genes12,989
Small non coding genes12,038
Long non coding genes941
Misc non coding genes10
Pseudogenes201
Gene transcripts76,329

Other

Genscan gene predictions34,357

About this species

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