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Clown anemonefish assembly and gene annotation

Assembly

The AmpOce1.0 assembly was submitted by Deakin University on November 2017. The assembly is on scaffold level, consisting of 7,803 contigs assembled into 6,405 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 324,210 while the scaffold N50 is 401,715.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_002776465.1

Gene annotation

The ocellaris clownfish (Amphiprion ocellaris), also known as the false percula clownfish or common clownfish, is a marine fish belonging to the family Pomacentridae, which includes clownfishes and damselfishes. Amphiprion ocellaris are found in different colors, depending on where they are located. For example, black Amphiprion ocellaris with white bands can be found near northern Australia, Southeast Asia, and Japan. Orange or red-brown Amphiprion ocellaris also exist with three similar white bands on the body and head. Amphiprion ocellaris can be distinguished from other Amphriphon species based on the number of pectoral rays and dorsal spines. Amphiprion ocellaris are known to grow about 110 mm long. Like many other fish species, females are, however, larger than males. The life cycle of Amphiprion ocellaris varies in whether they reside at the surface or bottom of the ocean. When they initially hatch, they reside near the surface. However, when Amphiprion ocellaris enter into the juvenile stage of life, they travel down to the bottom to find shelter in a host anemone. Once they find their anemone, they form a symbiotic relationship with them.

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

AssemblyAmpOce1.0, INSDC Assembly GCA_002776465.1, Nov 2017
Base Pairs880,720,895
Golden Path Length880,720,895
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,592
Non coding genes1,144
Small non coding genes1,124
Long non coding genes3
Misc non coding genes17
Pseudogenes37
Gene transcripts33,631

Other

Genscan gene predictions51,225

About this species