Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto

Abstract

Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).

Fig 1. Bi-directional variant calling and identification of putatively positive selected genes as described in materials and methods.

(A) Bi-directional variant calling pipeline between the two clones (GER, USA), (B) Ka/Ks ratio calculation pipeline.

Fig 2. Distribution of Ka:Ks ratio.

Blue circles represent orthologous pairs with a statistical significant (p < 0.05) Ka/Ks > 1. Red circles represent all genes with a Ka/Ks > 1. Black line denotes the boundary between genes with a Ka/Ks > 1 and all other genes carrying SNPs (Ka/Ks < 1). Inset indicates genes belonging to the significantly enriched pathways and carrying potentially deleterious mutations. CTSL; cathepsin, cynT; carbonic anhydrase, TST; thiosulfate/3-mercaptopyruvate sulfurtransferase, WBP1; oligosaccharyltransfe-rase complex subunit beta, E5.1.99.4; alpha-methylacyl-CoA racemase, ELOVL5: elongation of very long chain fatty acids protein 5, GULO; L-gulonolactone oxidase, ASIC1: acid-sensing ion channel 1, ANPEP; aminopeptidase N, FASN: fatty acid synthase, animal type.

Fig 3. Distribution of pathways enriched in putatively A) positively selected genes, and B) negatively selected genes in main and secondary KEGG biological categories.

Fig 4. Experimental RNA-seq design and number of genes expressed differently after exposure to 14 °C and 26 °C along with their function.

Genes previously reported in literature to be differentially expressed either under cold or heat stress are reported here along with a citation for the relevant study and the studied organism.