Genome-wide identification, evolution, and mRNA expression of complement genes in common carp (Cyprinus carpio).

Complement is a complex component of innate immune system, playing an important role in defense against pathogens and host homeostasis. The complement system has been comprehensively studied in mammals, however less is known about complement in teleost, especially in tetraploid common carp (Cyprinus carpio). In this study, a total of 110 complement genes were identified and characterized in common carp, which include almost all the homologs of mammalian complement genes. These genes were classified into three pathways (alternative pathways, lectin pathways and classical pathways), similar to those in mammals. Phylogenetic and selection pressure analysis showed that the complement genes were evolving-constrained and the function was conserved. Most of the complement genes were highly expressed in spleen, liver, brain and skin among the tested 12 health tissues of common carp. After Aeromonas hydrophila infection in the common carp, many members of complement genes were activated to bring about an immune response and expressed to against any pathogenic encroachment. Gene expression divergences which were found between two homoeologous genes suggested the functional divergences of the homoeologous genes after the 4R WGD event, revealing the evolutionary fate of the tetraploid common carp after the recent WGD.

The adaptive evolution of Leuciscus waleckii in Lake Dali Nur and convergent evolution of Cypriniformes fishes inhabiting extremely alkaline environments.

Leuciscus waleckii is widely distributed in Northeast Asia and has high economic value. The population in Lake Dali Nur can adapt to extremely alkaline-saline water with bicarbonate over 50 mmol/L (pH 9.6), thus providing an exceptional model for exploring the mechanisms of adaptive evolution under extreme alkaline environments. Here, we assembled a high-quality chromosome-level reference genome for L. waleckii from Lake Dali Nur. Based on the resequencing of 85 individuals from divergent populations, the historical population size of L.waleckii in Lake Dali Nur dramatically expanded in a thousand years approximately 13,000 years ago, and experienced a cliff recession in the process of adapting to the alkaline environment of Lake Dali Nur approximately 6,000 years ago. Genome scans between freshwater and alkaline populations further revealed the significant selective sweep regions from Lake Dali Nur, which harbour a set of candidate genes involved in hypoxia tolerance, ion transport, acid-base regulation and nitrogen metabolism. 5 alkali population-specific nonsynonymous mutations were identified in CA15 gene copies. In addition, two sites with convergent amino acid mutation were detected in the RHCG-a gene among several alkali environment adapted Cypriniformes fish. Our findings provide comprehensive insight into the genomic mechanisms of L. waleckii and reveal their adaptative evolution under extreme alkaline environments.

Genome wide identification of taste receptor genes in common carp (Cyprinus carpio) and phylogenetic analysis in teleost.

Taste receptors (TRs) are seven trans-membrane G protein-coupled receptors as well as the interface between internal and external milieus, which playing pivotal roles in nutrient identification and acquisition. To better understand the scope and function of tr gene family in common carp, one of the most economic and important breeding fish species, which has undergone an additional round of whole genome duplication (WGD), we characterized 13 tr gene homologues including eight type I and five type II taste receptor genes from common carp genome, which were more than any other teleosts. Phylogenetic and syntenic analysis revealed the evolution dynamics of tr gene family, which was highly conserved, though gene duplication and gene loss do exist recently. Furthermore, the motif and dN/dS analyses indicated that these receptors were under different negative selection pressure. Additionally, the gene expression divergences were observed in 12 health tissues of common carp, with a relatively high level in barbel and head kidney, demonstrating tissue-specific expression of tr genes in the tetraploidized genome. The overarching goals of this study were to identify the abundance of tr genes in common carp, compare the gene divergence among species with varied feeding habits and provide genomic resources for future studies on teleost taste sensation.