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Orange clownfish assembly and gene annotation

Assembly

The Nemo_v1 assembly was submitted by King Abdullah University of Science and Technology on April 2018. The assembly is on chromosome level, consisting of 1,047 contigs assembled into 365 scaffolds. From these sequences, 24 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 3,123,421 while the scaffold N50 is 38,416,550.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_003047355.1

Gene annotation

The orange clownfish (Amphiprion percula) also known as percula clownfish and clown anemonefish, is widely known as a popular aquarium fish. Like other clownfishes (also known as anemonefishes), it often lives in association with sea anemones. A. percula is associated specifically with Heteractis magnifica and Stichodactyla gigantea, and as larvae use chemical cues released from the anemones to identify and locate the appropriate host species to use them for shelter and protection. This causes preferential selection when finding their anemone host species. Although popular, maintaining this species in captivity is rather complex. The Great Barrier Reef Marine Park Authority regulates the number of collection permits issued to aquarium fish dealers who seek this, and other tropical fish within the Great Barrier Reef Marine Park. The symbiosis between anemonefish and anemones depends on the presence of the fish drawing other fish to the anemone, where they are stung by its venomous tentacles. The anemone helps the fish by giving it protection from predators, which include brittle stars, wrasses, and other damselfish, and the fish helps the anemone by feeding it, increasing oxygenation, and removing waste material from the host. Various hypotheses exist about the fish's ability to live within the anemone without being harmed. One study carried out at Marineland of the Pacific by Dr. Demorest Davenport and Dr. Kenneth Noris in 1958 revealed that the mucus secreted by the anemone fish prevented the anemone from discharging its lethal stinging nematocysts. A second hypothesis is that A. percula has acquired immunity towards the sea anemone’s toxins, and a combination of the two has been shown to be the case. The fish feed on algae, zooplankton, worms, and small crustaceans.

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

AssemblyNemo_v1, INSDC Assembly GCA_003047355.1, Apr 2018
Base Pairs908,939,294
Golden Path Length908,939,294
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,926
Non coding genes875
Small non coding genes849
Long non coding genes3
Misc non coding genes23
Pseudogenes39
Gene transcripts35,899

Other

Genscan gene predictions48,033

About this species