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Pike-perch assembly and gene annotation

Assembly

The SLUC_FBN_1 assembly was submitted by Leibniz Institute for Farm Animal Biology (FBN) on September 2019. The assembly is on scaffold level, consisting of 1,348 contigs assembled into 1,313 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 4,695,595 while the scaffold N50 is 4,929,547.

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

AssemblySLUC_FBN_1, INSDC Assembly GCA_008315115.1, Sep 2019
Base Pairs900,477,767
Golden Path Length900,477,767
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedDec 2019
Genebuild releasedMay 2020
Genebuild last updated/patchedJan 2020
Database version101.1

Gene counts

Coding genes24,521
Non coding genes1,262
Small non coding genes790
Long non coding genes455
Misc non coding genes17
Pseudogenes335
Gene transcripts63,087

Other

Genscan gene predictions57,963

About this species

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