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).