Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus
Open Access
- 28 December 2019
- Vol. 11 (1), 42
- https://doi.org/10.3390/genes11010042
Abstract
Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.Keywords
Funding Information
- Foundation for the National Institutes of Health (R15 EY029499-01A1, NIDCR R01-DE025033)
- National Science Foundation (DEB-1457630, GRFP 2016230010)
This publication has 60 references indexed in Scilit:
- Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus CavefishMolecular Biology and Evolution, 2013
- Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda)BMC Ecology and Evolution, 2013
- An Integrated Transcriptome-Wide Analysis of Cave and Surface Dwelling Astyanax mexicanusPLOS ONE, 2013
- De Novo Sequencing of Astyanax mexicanus Surface Fish and Pachón Cavefish Transcriptomes Reveals Enrichment of Mutations in Cavefish Putative Eye GenesPLOS ONE, 2013
- Evolution and development in cave animals: from fish to crustaceansWIREs Developmental Biology, 2012
- Genetic basis of eye and pigment loss in the cave crustacean, Asellus aquaticusProceedings of the National Academy of Sciences, 2011
- Chapter 8 Evolution and Development in the Cavefish AstyanaxPublished by Elsevier ,2009
- A Novel Role for Mc1r in the Parallel Evolution of Depigmentation in Independent Populations of the Cavefish Astyanax mexicanusPLoS Genetics, 2009
- The evolutionary significance of cis-regulatory mutationsNature Reviews Genetics, 2007
- Phylogeography of subterranean and surface populations of water lice Asellus aquaticus (Crustacea: Isopoda)Molecular Ecology, 2004