Expression analyses of cave mollies ( Poecilia mexicana ) reveal key genes involved in the early evolution of eye regression

Abstract

Eye regression occurs across cave-dwelling populations of many species and is often coupled with a decrease or loss in eye function. Teleost fishes are among the few vertebrates to undergo widespread colonization of caves and often exhibit eye regression with blindness. Cave populations of the poeciliid fish Poecilia mexicana (cave molly) exhibit reduced—albeit functional—eyes, offering the opportunity to investigate partial eye regression. We sequenced eye transcriptomes of cave and surface populations of P. mexicana to identify differentially expressed genes that potentially underlie eye regression in cave mollies. We identified 28 significantly differentially expressed genes, 20 of which were directly related to light sensitivity, eye structure and visual signaling. Twenty-six of these genes were downregulated in cave compared to surface populations. Functional enrichment analysis revealed eye-related gene ontologies that were under-represented in cave mollies. In addition, a set of co-expressed genes related to vision and circadian rhythm was correlated with habitat type (cave versus surface). Our study suggests that differential gene expression plays a key role in the beginning evolutionary stages of eye regression in P. mexicana , shedding further light on regressive evolution in cavefish.

Comparative eye and liver differentially expressed genes reveal monochromatic vision and cancer resistance in the shortfin mako shark (Isurus oxyrinchus)

“…Regarding signaling function genes they were involved in calcium channel mediating constitutive calcium ion entry (TRPM3), and sodium-dependent neutral amino acid transporter and also may have a role as transporter for neurotransmitter precursors into neurons (SLC6A15). The genes (top 10 ranked DEGs) found in the eye were different from those commonly found in the of other fishes [41,42], except CRYBA1. The gene CRYBA1 was present and also overexpressed in other transcriptome-eye shark [39].…”

Seeing in the swamp: hydrogen sulfide inhibits eye metabolism and visual acuity in a sulfide-tolerant fish

“…In a preliminary investigation, we did not observe any profound physical damage to the eye of K. marmoratus at approximately 400 µM of H 2 S (electronic supplementary material, figure S1). Interestingly, the H 2 S-tolerant cave-dwelling Poecilia mexicana has reduced eyes, possibly because they inhabit H 2 S-rich and low light environments [25]. By contrast, K. marmoratus have relatively large eyes for their body size and possess a rete mirabile (electronic supplementary material, figure S1) which would facilitate O 2 delivery to the eye.…”

microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide

“…Our new annotation of miRNAs also provides an important addition to the growing genomic resources for P. mexicana, which include a variety of transcriptome data sets (Kelley et al, 2012) and a draft reference genome that lacked miRNA annotations (Warren et al, 2018). Improving these resources has the potential to impact future research, since P. mexicana is not only studied in the context of adaptation and speciation in sulphide springs (Tobler et al, 2018), but also in the context of animal behaviour (Bierbach et al, 2013;MacLaren & Rowland, 2006;Marler & Ryan, 1997;Plath et al, 2004), predator-prey interactions (Bierbach et al, 2011;Tobler et al, 2007), sensory ecology (McGowan et al, 2019;Tobler et al, 2010), life history (Riesch et al, 2009(Riesch et al, , 2010 and the origin of unisexual species (Schartl et al, 1995;Schlupp, 2005). Comparing P. mexicana miRNAs to those of other teleost fishes, we found a number of orthologs across species.…”