De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachón Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye Genes

Abstract

Astyanax mexicanus, a teleost species with surface dwelling (surface fish) and cave adapted (cavefish) morphs, is an important model system in evolutionary developmental biology (evodevo). Astyanax cavefish differ from surface fish in numerous traits, including the enhancement of non-visual sensory systems, and the loss of eyes and pigmentation. The genetic bases for these differences are not fully understood as genomic and transcriptomic data are lacking. We here present de novo transcriptome sequencing of embryonic and larval stages of a surface fish population and a cavefish population originating from the Pachón cave using the Sanger method. This effort represents the first large scale sequence and clone resource for the Astyanax research community. The analysis of these sequences show low levels of polymorphism in cavefish compared to surface fish, confirming previous studies on a small number of genes. A high proportion of the genes mutated in cavefish are known to be expressed in the zebrafish visual system. Such a high number of mutations in cavefish putative eye genes may be explained by relaxed selection for vision during the evolution in the absence of light. Based on these sequence differences, we provide a list of 11 genes that are potential candidates for having a role in cavefish visual system degeneration.

Microsatellite Development and First Population Size Estimates for the Groundwater Isopod Proasellus walteri

“…[61,62]). While surprising at the site level, high diversity among sites, as is evidenced by numerous private alleles, was somewhat more expected.…”

“…However, Buhay & Crandal [33] documented changes in long-term N e of crayfishes rather than changes in contemporary N e . Other evidences come from reduced heterozygosity values in groundwater [61,62,71], but this reduction may not be systematic [72] nor readily interpretable in terms of N e [73]. Importantly, to solve this issue, alternative molecular methods such as Single Nucleotide Polymorphism detection and calling using RAD-tag sequencing [69] seem very promising as they may provide thousands of loci when it proves difficult to develop more than tens loci in most, including ours, microsatellite studies.…”

Life in the Underworld: Anchialine cave biology in the era of speleogenomics

“…For instance, Hinaux et al (2013) used RNASeq to show that the loss of vision in the Mexican cavefish Astyanax fasciatus is probably due to relaxed selective pressures on their visual genes, which showed numerous deleterious mutations. A similar occurrence was reported by Tierney et al (2015), who analyzed the transcriptomes of three cave-dwelling beetles and found evidence of convergent loss of opsin photoreceptor transcription by neutral processes.…”

Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses

“…From the feedback we received from our trainees, the final projects helped most of them to implement and improve their newly learned skills. Although it is not realistic to expect group publications solely based on the work performed during these 3-4 days, trainees can continue working on the final projects after the course, offering an important basis for subsequent research papers (Hinaux et al 2013).…”