| The Amur ide(Leuciscus waleckii),a Cyprinid species,is broadly distributed in Northeast Asia.Amur ide are extremely tolerant of highly alkai-saline waters.For example,the population in Lake Dali can adapt to extremely alkali–saline water with bicarbonate over 50 mmol/L and p H 9.6.The high alkalinity,salinity and p H of the alkali-saline waters have led to the evolution of specific phenotypic plasticity mechanisms in the Lake Dali population to reduce or resist the adverse effects of the stress environment,underpinned by a combination of genetic and epigenetic variation to mediate rapid adaptation to the environment.It is of great theoretical and practical importance to analyse the adaptive genetic mechanisms of the Amur ide in extreme alkali-saline environments,in order to breed new species tolerant to high alkalinity-salinity and promote the sustainable and high-quality development of aquaculture in China.In this study,we first collected a total of 14 individuals from the high alkali-sainle tolerant population of Lake Dali(DL),the freshwater population of the neighbouring Lake Ganggeng(GG)and the freshwater form from its historical origin,namely,the Songhua River(SH)and performed whole genome resequencing with an averahe fold-depth of 52.87×.We analyzed the nucleotide diversity and population structure among the three populations.Next,we identified the genomic selection regions and positively selected genes under the effect of local adaptation by eliminating spatial background variation and genome scans.Then,we performed selection pressure analysis on key regulatory genes.In order to explore the influence of epigenetic regulation(DNA methylation)on the phenotypic plasticity of alkalinity-salinity acclimation in Amur ide,an indoor stress experiment at 50 mmol/L carbonate alkalinity for 10 d was conducted on the Amur ide,with 30 d of freshwater(FW)transient feeding as control,and gill tissues were collected at 1 d(AW1),5 d(AW5)and 10 d(AW10)of stress for whole-genome DNA methylation sequencing at an average depth of 19.63×.DNA methylation dynamics were mapped at single-base resolution across the gill tissues,with comparative screening of differentially methylated genes among groups.The main results were as follows:1.A total of 679.82 Gb clean data and 38091163 high-quality single-nucleotide polymorphism loci were detected in the three populations.2.Nucleotide diversity and population structure analysis revealed that the DL and GG populations have lower nucleotide diversities and different genetic structures than those of the SH population.3.Selective sweeping showed 21 genes involved in osmoregulatory regulation(dlg1,vipr1,akt1,and gnai1),inflammation and immune responses(dlg1,brinp1,ctsl,traf6,akt1,stat3,gnai1,sec22 b,and psme4b),and cardiovascular development(traf6,psme4 b,stat3,akt1,and col9a1)to be associated with alkaline adaption of the DL population.4.Selective pressure methods(Code ML,MEME,and FEL)identified two functional codon sites of VIPR1 to be under positive selection in the DL population.The subsequent 3D protein modeling confirmed that these selected sites will incur changes in protein structure and function in the DL population.5.The whole-genome DNA methylation dynamics of Amur ide were mapped.The DNA methylation levels in the promoter region gradually decreased from the flanking region upstream of the transcription start site,reached a low peak at the transcription start site,and then increased and stabilized.6.In AW1 vs.FW group,differentially hyper-methylated genes in the promoter region were mainly enriched in metabolic processes,incluing purine metabolism,glycerolipid metabolism,amino sugar and nucleotide sugar metabolism,etc,and the differentially hypo-methylated genes were mainly enriched in inflammatory and immune responses,including ubiquitin-mediated proteolysis,PPAR signaling pathway,JNK/SAPK signaling,etc.The differentially hyper-methylated genes of the AW5 vs.FW group remained enriched in a large number of metabolic pathways similar to the AW1 vs.FW group,while the differentially hypo-methylated genes were mainly enriched in osmoregulatory pathways,including mineral absorption,Renin-angiotensin system and endocrine and other factor-regulated calcium reabsorption,etc.In AW10 vs.FW,no significant pathway enrichment of hyper-methylated and hypo-methylated genes.In this study,we analyzed the different genetic bases of alkali-saline phenotypic plasticity in Amur ide,scanned the genomic selection signal in different populations,analyzed the adaptive genetic variation in the selection signal region,and examined the DNA methylation differences in the gill tissue under alkali-saline stress environment.The results of this study provide molecular evidence of alkali-saline adaptation,which will be very useful for revealing the genetic basis of alkali-saline adaptation in Amur ide. |
PDF Full Text Request