Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution

EvoDevo

Research

Layla Freeborn¹  Sheri A. Sanders²  Dennis A. Sun³  Lubna Mulla⁴  Lizet Reyes Rodas⁴  Meredith E. Protas⁴  Haeli J. Lomheim⁵ 

[1] Center for Research Data and Digital Scholarship, University of Colorado Boulder, 80309, Boulder, CO, USA;Department of Biological Sciences, University of Notre Dame, 46556, Notre Dame, IN, USA;Department of Molecular and Cell Biology, University of California at Berkeley, 94720, Berkeley, CA, USA;Department of Natural Sciences and Mathematics, Dominican University of California, 94901, San Rafael, CA, USA;Department of Natural Sciences and Mathematics, Dominican University of California, 94901, San Rafael, CA, USA;Department of Biology, Georgetown University, 20057, Washington, DC, USA;

关键词: Cave;    Pigment;    Eye;    Troglomorphy;    Allele-specific expression;   

DOI  :  10.1186/s13227-023-00213-z

 received in 2022-11-26, accepted in 2023-04-15,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundTranscriptomic methods can be used to elucidate genes and pathways responsible for phenotypic differences between populations. Asellus aquaticus is a freshwater isopod crustacean with surface- and cave-dwelling ecomorphs that differ greatly in multiple phenotypes including pigmentation and eye size. Multiple genetic resources have been generated for this species, but the genes and pathways responsible for cave-specific characteristics have not yet been identified. Our goal was to generate transcriptomic resources in tandem with taking advantage of the species’ ability to interbreed and generate hybrid individuals.ResultsWe generated transcriptomes of the Rakov Škocjan surface population and the Rak Channel of Planina Cave population that combined Illumina short-read assemblies and PacBio Iso-seq long-read sequences. We investigated differential expression at two different embryonic time points as well as allele-specific expression of F1 hybrids between cave and surface individuals. RNAseq of F2 hybrids, as well as genotyping of a backcross, allowed for positional information of multiple candidate genes from the differential expression and allele-specific analyses.ConclusionsAs expected, genes involved in phototransduction and ommochrome synthesis were under-expressed in the cave samples as compared to the surface samples. Allele-specific expression analysis of F1 hybrids identified genes with cave-biased (cave allele has higher mRNA levels than the surface allele) and surface-biased expression (surface allele has higher mRNA levels than the cave allele). RNAseq of F2 hybrids allowed for multiple genes to be placed to previously mapped genomic regions responsible for eye and pigmentation phenotypes. In the future, these transcriptomic resources will guide prioritization of candidates for functional analysis.

【 授权许可】

CC BY   
© The Author(s) 2023. corrected publication 2023

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