Understanding the Genomic Basis of Adaptive Response to Variable Osmotic Niches in Freshwater Prawns: A Comparative Intraspecific RNA-Seq Analysis of Macrobrachium australiense

Abstract

Understanding the molecular basis of adaptive response to variable environmental conditions is a central goal of evolutionary biology. Here, we sought to identify potential outlier single nucleotide polymorphisms (SNPs) in 3 wild populations of a freshwater prawn (Macrobrachium australiense) that are exposed to differing osmotic niches by using a comparative transcriptomics approach. De novo assembly of approximately 542 million (75 nt) pair end reads collected from 10 individuals revealed 123396 longer contigs/transcripts of variable length, that showed 97.38% transcriptome assembly completeness. Differential gene expression analysis of major osmoregulatory genes revealed that calreticulin, Na⁺/H⁺ exchanger, and V-type (H⁺) ATPase showed the highest expression levels in the Blunder Creek (low ionic) population, while Crustacean cardiovascular peptide (CCP), Na⁺/K⁺-ATPase, Na⁺/K⁺/2Cl⁻ co-transporter (NKCC) and Na⁺/HCO₃⁻ exchanger showed the highest expression levels in the Bulimba Creek (higher ionic) population. In total, 16 gene ontology term categories were functionally enriched among the 3 studied populations. We identified 4144 raw and 835 high quality filtered SNPs in the 3 M. australiense populations, of which 84 SNPs were identified as outliers. Outliers were detected in 4 important osmoregulatory genes that include: calreticulin, Na⁺/H⁺ exchanger, Na⁺/K⁺-ATPase, and V-type-(H⁺)-ATPase. All outliers in the osmoregulatory genes were located in noncoding regulatory regions (untranslated regions) of the gene. We hypothesize that the outlier SNPs identified here in M. australiense populations exposed naturally to different osmotic conditions influence specific gene expression patterns that allow individuals to respond to local environmental conditions.

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