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Turquoise killifish assembly and gene annotation

Assembly

The Nfu_20140520 assembly was submitted by Leibniz Institute For Age Research - Fritz Lipmann on January 2016. The assembly is on chromosome level, consisting of 74,941 contigs assembled into 6,013 scaffolds. From these sequences, 19 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 19,950 while the scaffold N50 is 15,858,201.

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

AssemblyNfu_20140520, INSDC Assembly GCA_001465895.2, Dec 2015
Base Pairs1,242,518,059
Golden Path Length1,242,518,059
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2020
Genebuild releasedMay 2020
Genebuild last updated/patchedFeb 2020
Database version101.2

Gene counts

Coding genes23,428
Non coding genes1,402
Small non coding genes344
Long non coding genes1,048
Misc non coding genes10
Pseudogenes645
Gene transcripts57,281

Other

Genscan gene predictions54,597

About this species

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