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Fugu assembly and gene annotation

Takifugu rubripes, commonly known as the Japanese puffer, Tiger puffer, or torafugu, is distinguished by a very small genome which is in widespread use as a reference in genomics.

Assembly

The fTakRub1.2 assembly was submitted by SC on June 2019. The assembly is on chromosome level, consisting of 530 contigs assembled into 128 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 3,136,617 while the scaffold N50 is 16,705,553.

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

AssemblyfTakRub1.2, INSDC Assembly GCA_901000725.2, Jun 2019
Base Pairs384,110,215
Golden Path Length384,110,215
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJun 2019
Genebuild releasedDec 2019
Genebuild last updated/patchedAug 2019
Database version100.12

Gene counts

Coding genes21,411
Non coding genes2,178
Small non coding genes1,002
Long non coding genes1,170
Misc non coding genes6
Pseudogenes816
Gene transcripts55,740

Other

Genscan gene predictions31,037

About this species

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