is a characiform fish consisting of distinct surface dwelling (surface fish) and cave adapted (cavefish) forms. The ancestors of cavefish were isolated in caves about a million-year ago (Ma) and have since adapted to this extreme environment, which is characterized by constant darkness and food scarcity. Cavefish differ from their surface counterparts in numerous morphological, physiological and behavioral traits, the most striking being that cavefish lack functional eyes and are de-pigmented, and generally have lower metabolic rates than surface fish 
. Twenty-nine different cavefish populations have been discovered so far, and some of them were derived independently, allowing the study of parallel evolution 
. Cavefish and surface fish are inter-fertile, making Astyanax mexicanus
an outstanding genetic model for microevolution studies 
. All the phenotypic changes in cavefish, including the loss of eyes and pigmentation, may be explained by different evolutionary mechanisms. The two main hypotheses are: (1) positive selection, either direct or indirect, for traits that are beneficial in the dark, (2) neutral evolution by genetic drift, for traits that are not under selection 
Neither genomic nor transcriptomic data are currently available for Astyanax mexicanus.
The closest model species with a sequenced genome is the zebrafish Danio rerio
, a cypriniform. The common ancestor of characiforms and cypriniforms diverged at least 100 Ma 
and could even be more distantly related (>200 Ma), rendering some comparisons difficult 
. The genetic bases of adaptation to life in caves have thus remained elusive. From studies in other model organisms, it was proposed that phenotypic evolution can be explained in part by changes in non-coding regulatory sequences: for example, in stickleback Gasterosteus aculeatus
, pelvic spine reduction during the transition from marine to freshwater environments is due to the deletion of a Pitx1
. However, phenotypic changes can also be based on mutations in coding sequences. For instance, the reduction or loss of pigmentation in Astyanax mexicanus
cavefish is due to mutations in the Mc1r
coding sequences 
. A few other coding sequences were investigated in Astyanax
in attempts to understand the genetic bases for cavefish eye degeneration. On the one hand, the “master gene” for eye development, Pax6
, was found to be identical in the two populations 
, while on the other hand, opsin gene sequences were found to accumulate C->T transitions in cavefish, as a signature of pseudogenes formation 
. These case studies are still limited to a small number of genes, due to the lack of sequence data. This situation will change in a near future, due to the ongoing Pachón cavefish genome project at the Washington University in Saint Louis.
In the context of a paucity of sequence information, understanding the evolutionary history of Astyanax mexicanus
populations is also challenging. Relying on 6 microsatellite loci and mitochondrial DNA, it was shown that not all cave populations share the same origin 
. More recently, using 26 microsatellite markers, Bradic et al. proposed a model with five independent origins of cave-adapted Astyanax
in Mexico, with two invasion “waves” of surface fish into the subterranean environment establishing “old” and “new” cave populations 
. Pachón cavefish, which shows the most severe eye degeneration and de-pigmentation phenotypes is the most studied cave population and belongs to the “old” populations 
. In previous studies of the various cavefish populations, the genetic diversity was generally found to be lower in cavefish than in surface fish 
, possibly resulting from small effective population sizes because of food and space limitations or from population bottlenecks due to sporadic environmental degradations 
. Obtaining large sequence datasets on Astyanax mexicanus
surface fish and cave populations to assess their genetic diversity would therefore also help understand their evolutionary history.
Here we have sequenced cDNA libraries from several different developmental stages of Astyanax mexicanus
surface fish and Pachón cavefish. The crucial need for long transcript sequences and the lack of a close reference genome led us to use the Sanger sequencing method. The inclusion of different developmental stages allowed scanning most of the developmental transcriptome, as well as the successive steps of eye development and degeneration in Pachón cavefish. About 200,000 clones were sequenced, providing a new resource for the Astyanax
research community. These transcriptomic sequences were then used to compare the level of polymorphism in the coding sequences of the two Astyanax
morphs at a larger scale than what was previously possible 
, and to identify fixed differences in coding sequences between surface fish and cavefish, which are candidates for being involved in some of their phenotypic differences.