Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape

Abstract

In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil’s geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.

Gene expression of Tasmanian devil facial tumors differs among host populations

“…Although DFTD infection produced no transcriptomic response in lip tissues for either sex, we found several genes that were differentially expressed between males and females generally, regardless of infection status. Consistent with previous work comparing sexes in uninfected devils [71], the X-linked gene FRMD7 was downregulated in males (log2FC = -4.01). FRMD7 is putatively involved in fatty acid metabolism and has been associated with skin disorders, serving as a potential factor in differential susceptibility between sexes to DFTD [71].…”

Disease swamps molecular signatures of genetic‐environmental associations to abiotic factors in Tasmanian devil ( Sarcophilus harrisii ) populations

“…We hypothesized that DFTD would serve as an extremely selective event as it is nearly 100% lethal (Hamede et al 2015) and can produce a rapid adaptive response (Epstein et al 2016;Wright et al 2017;Margres et al 2018a, b) that could swamp pre-disease allele frequency correlations with the abiotic environment detected with GEAs. Indeed, variation in allele frequencies of loci linked to candidate genes among devil populations prior to DFTD arrival appeared to be strongly associated with surface area of water among our coastal and inland populations (Tables S7-S9; Fraik et al 2019). However, following disease arrival these GEAs were not detected.…”

“…Indeed, variation in allele frequencies of loci linked to candidate genes among devil populations prior to DFTD arrival appeared to be strongly associated with surface area of water among our coastal and inland populations (Tables S7–S9; Fraik et al. 2019). However, following disease arrival these GEAs were not detected.…”

“…A previous transcriptomics studies of Tasmanian devil populations showed significant enrichment of differential expression of pre‐disease candidate genes associated with environmental variation between coastal and inland populations (Fraik et al. 2019). Strong genetic‐environmental associations across devil populations throughout their heterogeneous geographic range provide evidence for the presence of local adaptive genetic variation.…”

Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense

“…As we all know, the initial fuzz fibers are entangled with the lint fibers, and the separation of fuzz fibers or surface layer from the cotton ovules is also at risk of being interfered with by the lint fibers. Members of co-expressed gene modules usually have similar expression trends, and gene co-expression analysis is often used to obtain candidate gene sets related to specific developmental stages or important traits [ 63 , 64 , 65 ]. Based on the difference in the development process of lint fibers and fuzz fibers, an expression pattern closely related to the fuzz initiation process was revealed in our research.…”