Fugu assembly and gene annotation

Assembly

The FUGU5 assembly was submitted by The Fugu Genome Sequencing Consortium on October 2011. The assembly is on chromosome level, consisting of 30,861 contigs assembled into 7,091 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 52,883 while the scaffold N50 is 928,938.

Other assemblies

Gene annotation

Takifugu rubripes, commonly known as the Japanese puffer, Tiger puffer, or torafugu (Japanese: 虎河豚), is a pufferfish in the genus Takifugu. It is distinguished by a very small genome that has been fully sequenced because of its use as a model species and is in widespread use as a reference in genomics.

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

AssemblyFUGU 4.0, Jun 2005
Base Pairs393,312,790
Golden Path Length393,312,790
Annotation methodFull genebuild
Genebuild startedNov 2007
Genebuild releasedMar 2008
Genebuild last updated/patchedMay 2010
Database version94.4

Gene counts

Coding genes18,523
Pseudogenes162
Gene transcripts48,706

Other

Genscan gene predictions29,699

About this species