Positively selected genes in the genome
In addition to significant gene family dynamics, genes subject to positive selection also denote environmental adaptation. When comparing with the other two Triplophysa species, genes with evidences of positive selection were identified. As a result, a set of 898 candidate genes, likely subject to positive selection, were identified (Table S7).
Salinity change is a key driving force for the adaptation of the fishes endemic to Lake Dali Nur, with ion channels and aquaporins thought to be pivotal players in salinity stress conditions. Two piezo-type mechanosensitive genes (FAM38: Tdalaica.Chr01.107; Tdalaica.Chr08.21) associated with ion channels, and the enriched calcium signaling pathway (KEGG: map04020, Table S8), associated with positively selected genes, may partially explain the adaptation of T. dalaica to extreme alkaline environments. Paracellular transportation is another mechanism key to the maintenance of both ion homeostasis and acid-base balance. KEGG analyses suggest that positively selected genes participate in a number of ways to paracellular permeability pathways, including ECM-receptor (KEGG: map04512), cell adhesion molecules (CAMs) (KEGG: map04514), vascular endothelial growth factor (VEGF) (KEGG: map04370), and focal adhesion (KEGG: map04510), each of which was significantly enriched (Table S8).
Previous studies have reported that both carbonic anhydrase (CA) and sodium bicarbonate cotransport carriers (Na+/ HCO3- cotransporter, Solute Carrier4A4, SLC4A4 ) can mediate HCO3- transport; an important mechanism through which fish tolerate high alkali environments and export HCO3- from the body (Purkerson & Schwartz, 2007; Romero, Fulton, & Boron, 2004). CA is a zinc-containing metal enzyme predominantly involved in various biological osmotic processes, including permeability regulation, ion regulation, and acid-base regulation, such as CO2rehydration: CO2+H2O ⇌ H2CO3 ⇌ H++HCO3. A previous study conducted a similar investigation in Oncorhynchus mykiss, finding that expression levels of the CA gene were up-regulated under saline-alkali stress; indicating an important relationship between the CA gene and ion regulation (Goss, Wood, Laurent, & Perry, 1994). We found that two CA genes (Tdalaica.Chr17.484: CAV , Tdalaica.Chr24.506: CAXVI ), and one SLC4A4 gene (Tdalaica.Chr04.806:SLC4A4 ) were in a positive selection cluster (Table S7). The natriuretic peptide (NP) system is a key endocrine system involved in osmoregulation and ion homoeostasis in vertebrates, while atrial natriuretic peptide (ANP) has been confirmed as the primary sodium regulating hormone in eels (Cao et al., 2009). Two ANP genes (Tdalaica.Chr18.955, Tdalaica.Chr02.422) are in a positive selection cluster (Table S7), which may play a pivotal role in the response to regulate sodium in T. dalaica.
Hypoxia inducible factor 1 alpha (HIF-1a) acts as a key transcriptional activation factor in the hypoxic response regulation mechanism, which enhances the body’s tolerance to low oxygen by controlling the expression of genes related to physiological processes, such as glucose transport and sugar leaven (Haase, 2013). HIF-1 signaling pathway (KEGG: map04066) was significantly enriched in positively selected genes, suggesting it may play a pivotal role in the response to high altitude hypoxia (Table S8).
In a previous study, growth hormone (GH) and insulin-like growth factor I (IGFI) were involved in the regulation of ion homeostasis and salinity acclimation (Cao et al., 2009), with fibroblast growth factors (FGFS) behaving as important modulators of paracellular permeability regulation. We also found one IGFI gene, and three FGFS genes, subject to positive selection, providing further evidence of the involvement of these hormones in the regulation of ion homeostasis and salinity acclimation (Table S7).