RNA-seq analysis of blood from cave- and surface-dwelling Astyanax morphs reveal diverse transcriptomic responses to normoxic rearing

Abstract

Adaptive responses to hypoxia are likely accompanied by highly diverse changes in gene expression. Here, we examined the transcriptomic regulation in blood samples derived from independently-derived captive cave-dwelling fish. These fish are members of the species Astyanax mexicanus, which comprises two morphs: an obligate subterranean form, and a "surface-dwelling" form that lives in rivers and streams located near cave localities. These morphs diverged ∼20,000-200,000 years ago, and cavefish derived from multiple, distinct cave localities have adapted to life in hypoxic waters. Here, we focused on captive-reared Astyanax morphs since elevated hemoglobin levels persist in cavefish despite rearing in the normoxic conditions of a laboratory. A GO enrichment analysis revealed several instances of convergent gene regulation between some, but not all, cavefish populations. This finding suggests that different gene expression patterns have evolved in response to hypoxia across geologically-distinct cave localities. Additionally, we identified differential regulation of numerous genes of the canonical hypoxic response pathway. Interestingly, some genes activating this pathway were expressed lower in captive-reared cavefish. These patterns of gene expression may have evolved in cavefish as a consequence of negative pleiotropic consequences associated with prolonged hif gene expression. At present, it is unknown whether this finding is a function of captivity, or whether these expression patterns are also present in wild populations. Collectively, this work provides new insights to the transcriptomic regulation of hypoxia tolerance using a cavefish model evolving in distinct oxygenated environments.

Keywords: GO terms; enrichment analysis; hypoxia; normoxia; subterranean.

FIGURE 1

GO Enrichment revealed many shared and unique terms across cave populations relating to oxygen transport and immune function. Statistically overrepresented terms in Tinaja and Pachón cavefish compared to surface fish largely represented oxygen binding and transport. The majority of overrepresented terms in Pachón and Chica cavefish related to immune function. Interestingly, there were no overlapping terms between Tinaja and Chica compared to surface fish. The distinct geography and environmental histories of these caves have likely impacted global gene expression patterns differently in Astyanax cavefish.