The Japanese medaka (Oryzias latipes) genome, which has been sequenced by whole-genome shotgun sequencing and by using the Ramen assembler, is approximately 700Mb in length and comprises 24 pairs of chromosomes; 2 metacentric, 8 submetacentric, 1 subtelocentric and 13 acrocentric chromosomes in haploid condition. The genome sequencing and assembly for MEDAKA1 (October 2005) were provided by the National Institute of Genetics (NIG) and the University of Tokyo.
This Ensembl website presents sequence data provided by the two institutes. It also displays their gene set together with the Ensembl gene set and related analysis. See the data release policy for the medaka genome.
The gene set for Medaka was built using a modified version of the standard Ensembl genebuild pipeline. The species-specific sequence resources (medaka cDNA and protein) are very limited, so the majority of gene models are based on genewise alignments of proteins from other species that are genetically distant to medaka. To improve accuracy, genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Medaka cDNAs were aligned and used to add UTRs to the genewise predictions where possible. The gene models were then assessed by generating sets of potential orthologs to genes from other species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs and used to improve the gene models. Finally, additional genes were predicted using medaka EST evidence, and medaka ESTs were used to add UTRs to the gene set where possible.
General information about this species can be found in Wikipedia.
|Assembly||HdrR, Oct 2005|
|Golden Path Length||869,000,216|
|Annotation method||Full genebuild|
|Genebuild started||May 2006|
|Genebuild released||Oct 2006|
|Genebuild last updated/patched||Apr 2013|
|Non coding genes||759|
|Small non coding genes||748|
|Misc non coding genes||11|
|Genscan gene predictions||123,380|