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Spiny chromis assembly and gene annotation

Assembly

The ASM210954v1 assembly was submitted by King Abdullah University of Science and technology on April 2017. The assembly is on scaffold level, consisting of 159,493 contigs assembled into 30,414 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 16,099 while the scaffold N50 is 334,400.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_002109545.1

Gene annotation

Acanthochromis polyacanthus, the spiny chromis damselfish, is a species of damselfish from the western Pacific. It is the only member of its genus.

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

AssemblyASM210954v1, INSDC Assembly GCA_002109545.1, Apr 2017
Base Pairs991,584,656
Golden Path Length991,584,656
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes24,027
Non coding genes509
Small non coding genes490
Long non coding genes3
Misc non coding genes16
Pseudogenes29
Gene transcripts35,487

Other

Genscan gene predictions58,434

About this species