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Red-bellied piranha assembly and gene annotation

Assembly

The Pygocentrus_nattereri-1.0.2 assembly was submitted by McDonnell Genome Institute on July 2016. The assembly is on scaffold level, consisting of 325,620 contigs assembled into 283,518 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 57,732 while the scaffold N50 is 1,440,044.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001682695.1

Gene annotation

The red-bellied piranha, also known as the red piranha (Pygocentrus nattereri), is a species of piranha native to South America, found in the Amazon, Paraguay, Paraná and Essequibo basins, as well as coastal rivers of northeastern Brazil. This fish is locally abundant in its freshwater habitat. They are omnivorous foragers and feed on insects, worms, crustaceans and fish. They are not a migratory species, but do travel to seek out conditions conducive to breeding and spawning during periods of increased rainfall. Red-bellied piranhas often travel in shoals as a predatory defense, but rarely exhibit group hunting behavior. Acoustic communication is common, and is sometimes exhibited along with aggressive behaviors. Through media influence, the red-bellied piranha has developed a reputation as a ferocious predator, though this is not actually the case. They are a popular aquarium fish.

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

AssemblyPygocentrus_nattereri-1.0.2, INSDC Assembly GCA_001682695.1, Jul 2016
Base Pairs1,285,352,492
Golden Path Length1,285,352,492
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.102

Gene counts

Coding genes26,734
Non coding genes3,319
Small non coding genes3,269
Long non coding genes20
Misc non coding genes30
Pseudogenes51
Gene transcripts41,365

Other

Genscan gene predictions69,573

About this species