Physiological genomics of dietary adaptation in a marine herbivorous fish

Abstract

Adopting a new diet is a significant evolutionary change and can profoundly affect an animal's physiology, biochemistry, ecology, and its genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, the monkeyface prickleback (Cebidichthys violaceus). We sequenced and assembled its genome and digestive transcriptome and revealed the molecular changes related to important dietary enzymes, finding abundant evidence for adaptation at the molecular level. In this species, two gene families experienced expansion in copy number and adaptive amino acid substitutions. These families, amylase, and bile salt activated lipase, are involved digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids. Main Populations exposed to new environments often experience strong natural selection (e.g., Herrel et al. 2008). Comparing closely related species has been an effective perspective in pinpointing changes that drive adaptation (Dasmahapatra et al. 2012; Lamichhaney et al. 2015). In its most powerful incarnation, the comparative method links variation at the genetic level to molecular phenotypes that in turn change how whole organisms interact with their environments, revealing for example adaptation to new abiotic factors (Protas et al. 2006; Chakraborty and Fry 2015; Peichel and Marques 2017; Tong et al. 2017; Chen et al. 2018), changes in diet (Harris and Munshi-South 2017; Hsieh et al. 2017; Zepeda-Mendoza et al. 2018), and exposure to pollution (Vega-Retter et al. 2018). In animals, digestion is an ideal model phenotype because it is central to fitness, is understood in many species at genetic, molecular, biochemical, and physiological levels, and is a trait that shows abundant variation throughout animal evolution (Karasov and Martinez del Rio 2007). While studies of animal digestion have yielded insights into the physiology and biochemistry of adaptation, untangling its genetic basis is contingent on the availability and quality of genomic resources, which have traditionally been lacking in nonmodel species. Advances in genome technology have improved the quality and decreased the cost of obtaining sequences, stimulating the production of genome assemblies and catalyzing genetic discoveries for a diverse array of non-model organisms.Here we describe the genetic changes accompanying acquisition of an herbivorous diet in the marine intertidal fish, Cebidichthys violaceus. To do this we generated a physiological genomics dataset for this non-model species, including a highly contiguous and complete genome, the transcriptomes of digestive and hepatic tissues, and digestive enzyme activity levels.

Comparative transcriptomics reveal tissue level specialization towards diet in prickleback fishes

“…Hence, there is clear evidence that the herbivorous X. mucosus H not only displays a longer gut, but has genes under selection that contribute to greater epithelial surface area, all of which allow them to thrive on an algal diet. The pyloric ceca and mid-intestine are similar in function, as both are highly absorptive Heras et al 2020), and therefore, finding genes that express proteins involved with increasing surface area in the pyloric ceca agrees with the function of that tissue.…”

“…To address this research gap, we took a systems approach by integrating nutritional physiology and transcriptomics to better understand digestive system plasticity in response to dietary perturbations. In addition to changes in gene expression, fishes can certainly have mutational or gene copy number differences that can help explain physiological and biochemical variation among them, thus highlighting the importance of a modern molecular approach, like transcriptomics (German et al 2016;Heras et al 2020;Betancor et al 2018). RNA-seq using the Illumina high-throughput sequencing platform can provide whole de novo transcriptome information, gene functional information, and the molecular mechanisms of biological processes, including those related to digestion and metabolism, without requiring a reference genome (Martin et al 2016;Martin and Król 2017;Qi et al 2011).…”

“…1; German et al 2015;Kim et al 2014). Moreover, there is a rich literature developing on the digestive physiology (German et al 2004(German et al , 2014(German et al , 2015German and Horn 2006;Kim et al 2014) and genomics (German et al 2016;Heras et al 2020) of these species, providing ample opportunity to test for dietary specialization. We studied four closely-related, intertidal stichaeid species with different diets: Xiphister mucosus (herbivore), X. atropurpureus (omnivore), Phytichthys chirus (omnivore), and Anoplarchus purpurescens (carnivore).…”

“…Based on previous investigations of prickleback digestive physiology, genetics of amylase genes, and a genome of the herbivorous Cebidichthys violaceus, we expected to find signatures of dietary specialization in the different fish tissues (Tables 1, 2; German et al 2014German et al , 2004German et al , 2015German and Horn 2006;Heras et al 2020). Beyond the intestinal tissues, in which we predicted to observe evidence of selection on digestive enzyme genes (Table 1), and differences in gene expression in response to laboratory diet shifts (Table 2), the liver may provide insight into metabolic pathways favored by the different species with different diets, and whether those can shift when the animals are consuming different nutrient loads in the laboratory (Yang et al 2017;Merkin ).…”

Fish Transcriptomics: Applied to Our Understanding of Aquaculture

“…In addition, due to external fertilization and high fecundity in many aquaculture species serve as better candidates for gene editing as compared to terrestrial animals (Gratacap et al 2019). More genomic and transcriptomic studies are being produced with species that naturally have an herbivorous diet such as the monkeyface prickleback fish (Cebidichthys violaceus; Heras et al 2018). Although this is not a widely cultured fish, a better understanding of organisms that can digest and acquire nutrients from an herbivorous diet, can allows us to use gene editing tools in aquaculture species to ensure that genes that aide in the digestion of plant material obtain the proper nutrients and reduce the risk of ANF contribution which may have negative effects on the health of fishes.…”