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Tongue sole assembly and gene annotation

Assembly

The Cse_v1.0 assembly was submitted by Beijing Genomics Institute on January 2014. The assembly is on chromosome level, consisting of 62,912 contigs assembled into 31,181 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 27,008 while the scaffold N50 is 509,861.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000523025.1

Gene annotation

Cynoglossus is a genus of fish in the family Cynoglossidae. Most species are indigenous to the Indo-Pacific region, but they also occur in a few in warmer parts of the East Atlantic. They are commonly found in shallow waters on a muddy or sandy bottom, including estuaries and a few species are restricted to fresh water. One species Cynoglossus sinusarabici has invaded the Mediterranean Sea through the Suez Canal from the Red Sea, a process known as Lessepsian or Erythrean migration.

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

AssemblyCse_v1.0, INSDC Assembly GCA_000523025.1, Jan 2014
Base Pairs470,199,494
Golden Path Length470,199,494
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes21,372
Non coding genes412
Small non coding genes395
Long non coding genes2
Misc non coding genes15
Pseudogenes27
Gene transcripts34,435

Other

Genscan gene predictions33,207

About this species