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Indian medaka assembly and gene annotation

Assembly

The Om_v0.7.RACA assembly was submitted by Sungkyunkwan University on February 2018. The assembly is on scaffold level, consisting of 56,275 contigs assembled into 8,603 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 30,057 while the scaffold N50 is 23,737,187.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_002922805.1

Gene annotation

Oryzias is a genus of ricefishes native to fresh and brackish water in east and south Asia. Some species are widespread and the Japanese rice fish (O. latipes) is commonly used in science as a model organism, while others have very small ranges and are threatened. They are small, up to 8 cm (3.1 in) long, and most are relatively plain in colour.The genus name Oryzias is a reference to the scientific name for rice, Oryza.They have an unusual reproductive behavior where the female facultatively carries the eggs in a cluster at the pelvic or anal fins for a period after they have been fertilized.

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

AssemblyOm_v0.7.RACA, INSDC Assembly GCA_002922805.1, Feb 2018
Base Pairs779,452,910
Golden Path Length779,452,910
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.07

Gene counts

Coding genes23,543
Non coding genes450
Small non coding genes397
Long non coding genes4
Misc non coding genes49
Pseudogenes26
Gene transcripts36,821

Other

Genscan gene predictions48,512

About this species