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Bicolor damselfish assembly and gene annotation

Assembly

The Stegastes_partitus-1.0.2 assembly was submitted by Aquatic Genome Models on May 2014. The assembly is on scaffold level, consisting of 42,060 contigs assembled into 5,818 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 43,010 while the scaffold N50 is 411,659.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000690725.1

Gene annotation

Stegastes partitus or the bicolor damselfish is a species of bony fish in the family Pomacentridae found near the sea bed on shallow rocky and coral reefs in the Caribbean Sea, the Gulf of Mexico and off the coasts of Florida.The bicolor damselfish can grow to about 10 cm (3.9 in). The head and the front half of the body are dark grey or black and the rear half is pale, usually with some yellow, with regional variations in the coloring. The large dorsal fin has 12 spines and 14-17 soft rays. The anal fin is also large and has two spines and 13-15 soft rays.Unlike most other members of the genus Stegastes which eat filamentous algae, the bicolor damselfish feeds on plankton. It forms loose groups of up to twenty individuals and defends a territory over a rocky reef with plenty of crevices in which to lurk.

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

AssemblyStegastes_partitus-1.0.2, INSDC Assembly GCA_000690725.1, May 2014
Base Pairs800,491,834
Golden Path Length800,491,834
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,089
Non coding genes461
Small non coding genes447
Long non coding genes3
Misc non coding genes11
Pseudogenes43
Gene transcripts31,970

Other

Genscan gene predictions49,204

About this species