Cave fish assembly and gene annotation

Assembly

The blind cave fish (Astyanax mexicanus) genome sequence was produced by Washington University. The genome is 1Gb in length, consisting of 10,735 toplevel sequences, all of which are unplaced scaffolds (from 121,345 contigs). The N50 of the scaffolds is 1.5 Mb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000372685.1

Gene annotation

The gene set was built using a mixed approach. Due to the lack of species specific sequences and the availability of RNASeq data for blind cave fish from Washington University, the final gene set comprises models based on orthologous proteins from the vertebrate division of UniProtKB, longest translations of some stickleback and zebrafish gene models from Ensembl 72, as well as models from RNASeq data.

The RNASeq data only contained samples from the entire organism, not individual tissues. 13,097 gene models were made exclusively from RNASeq data. The data were also used to add UTR to gene models. The total gene set contains 23,042 protein-coding genes with a further 709 ncRNAs and 21 pseudogenes. You can find more information on how we build the gene models from RNASeq data here.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAstMex102, INSDC Assembly GCA_000372685.1, Apr 2013
Database version81.102
Base Pairs964,248,202
Golden Path Length1,191,242,572
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedApr 2013
Genebuild releasedDec 2013
Genebuild last updated/patchedDec 2013

Gene counts

Coding genes23,042
Non coding genes709
Small non coding genes694
Misc non coding genes15
Pseudogenes21
Gene transcripts24,428

Other

Genscan gene predictions39,152