| China possesses approximately 46 million hectares of low-lying saline-alkaline water resources. The high alkalinity and pH of these saline-alkaline water bodies can induce respiratory alkalosis and metabolic ammonia toxicity in aquatic organisms. The development and utilization of these resources not only could expand aquaculture space but also improve aquatic ecosystems and provide additional economic benefits. The Amur ide (Leuciscus waleckii) is a well-known indigenous fish species in northern China, with the Dali Lake population representing a small group characterized by low genetic diversity. Its phenotypic plasticity may be achieved through abundant epigenetic variation. This study preliminarily investigated the expression mechanisms of DNA cytosine-5-methyltransferase (DNMT) gene family in the adaptation of Leuciscus waleckii to saline-alkaline environments by integrating genomic and transcriptomic data, combining bioinformatics analysis with experimental validation. A total of seven dnmt gene family members were identified in the Leuciscus waleckii genome, distributed across five chromosomes, with dnmt3bb.1, dnmt3bb.2, and dnmt3bb.3 exhibiting a tightly linked arrangement. Phylogenetic and protein motif analyses revealed that dnmt3a and dnmt3b family members share high homology, whereas dnmt1 is evolutionarily distant from other members. The seven dnmt genes in Leuciscus waleckii clustered into three major branches: (1) dnmt3ab, dnmt3aa, and dnmt3bb.1 formed one subgroup; (2) dnmt3bb.2 and dnmt3bb.3, with close phylogenetic relationships, clustered together; and (3) dnmt1 and dnmt3ba grouped into a separate branch. Comparative analysis across species indicated that all dnmt isoforms in Leuciscus waleckii were closely related to those of other Cyprinidae species, such as zebrafish and grass carp. Furthermore, dnmt3ab, dnmt3bb.1, and dnmt3bb.2 exhibited divergent evolutionary relationships among euryhaline, marine, and freshwater fish, with functional characteristics potentially more aligned with marine and euryhaline species rather than freshwater fish. Expression analysis demonstrated that while most dnmt genes exhibited similar expression patterns across different populations, dnmt3ab displayed a unique alkalinity-responsive profile in the alkaline-water population, with its expression level significantly positively correlated with alkalinity gradients (P < 0.05). Population genetic analysis based on whole-genome resequencing data identified significantly differentiated SNPs (Fst top 10%, P < 0.05) between alkaline-water and freshwater populations. The average Fst value for all SNPs in the dnmt gene family was 0.173862, with dnmt3ab harboring a significantly higher number of differentiated SNPs than other dnmt members, along with a trend toward homozygous genotypes.
In conclusion, this study identified distinct dnmt isoforms in Leuciscus waleckii and their selected loci involved in alkaline adaptation. The phylogenetically related dnmt3ab and dnmt3bb.1 may participate in DNA methylation modifications of specific downstream target genes during the alkaline adaptation of Dali Lake Leuciscus waleckii. These findings lay the foundation for further exploration of key candidate genes susceptible to methylation modifications and their specific methyltransferases or interacting transcription factors, while also providing a theoretical framework for systematically deciphering the molecular functions of the dnmt gene family in fish. |
