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Cave fish assembly and gene annotation

The Mexican tetra or blind cave fish (Astyanax mexicanus) is a freshwater fish of the family Characidae of the order Characiformes. The type species of its genus, it is native to the Nearctic ecozone, originating in the lower Rio Grande and the Neueces and Pecos Rivers in Texas, as well as the central and eastern parts of Mexico.

The eyed and eyeless forms of A. mexicanus, being members of the same species, are closely related and can interbreed making this species an excellent model organism for examining convergent and parallel evolution, regressive evolution in cave animals, and the genetic basis of regressive traits. This, combined with the ease of maintaining the species in captivity, has made it the most studied cavefish and likely also the most studied cave organism overall.


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

Other assemblies

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.



AssemblyAstMex102, INSDC Assembly GCA_000372685.1, Apr 2013
Base Pairs964,248,202
Golden Path Length1,191,242,572
Annotation methodFull genebuild
Genebuild startedApr 2013
Genebuild releasedDec 2013
Genebuild last updated/patchedDec 2013
Database version99.102

Gene counts

Coding genes23,042
Gene transcripts24,428


Genscan gene predictions39,152

About this species