Whole-genome resequencing of three Coilia nasus population reveals genetic variations in genes related to immune, vision, migration, and osmoregulation

Abstract

Background: Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. Based on morphological and ecological researches of C. nasus, two ecotypes were identified. One is the anadromous population (AP). The sexually mature fish run thousands of kilometers from marine to river for spawning. Another one is the resident population which cannot migrate. Based on their different habitats, they were classified into landlocked population (LP) and sea population (SP) which were resident in the freshwater lake and marine during the entire lifetime, respectively. However, they have never been systematically studied. Moreover, C. nasus is declining sharply due to overfishing and pollution recently. Therefore, further understandings of C. nasus populations are needed for germplasm protection.

Results: Whole-genome resequencing of AP, LP, and SP were performed to enrich the understanding of different populations of C. nasus. At the genome level, 3,176,204, 3,307,069, and 3,207,906 single nucleotide polymorphisms (SNPs) and 1,892,068, 2,002,912, and 1,922,168 insertion/deletion polymorphisms (InDels) were generated in AP, LP, and SP, respectively. Selective sweeping analysis showed that 1022 genes were selected in AP vs LP; 983 genes were selected in LP vs SP; 116 genes were selected in AP vs SP. Among them, selected genes related to immune, vision, migration, and osmoregulation were identified. Furthermore, their expression profiles were detected by quantitative real-time PCR. Expression levels of selected genes related to immune, and vision in LP were significantly lower than AP and SP. Selected genes related to migration in AP were expressed significantly more highly than LP. Expression levels of selected genes related to osmoregulation were also detected. The expression of NKAα and NKCC1 in LP were significantly lower than SP, while expression of NCC, SLC4A4, NHE3, and V-ATPase in LP was significantly higher than SP.

Conclusions: Combined to life history of C. nasus populations, our results revealed that the molecular mechanisms of their differences of immune, vision, migration, and osmoregulation. Our findings will provide a further understanding of different populations of C. nasus and will be beneficial for wild C. nasus protection.

Keywords: Coilia nasus populations; Genetic variation; Genome resequencing; Migration; Selective sweeping.

Fig. 1

Statistics of SNPs and InDels. A SNP types. B Numbers of homologous and heterozygous SNPs. C Numbers of insertion and deletion on genome. D Numbers of homologous and heterozygous InDels on genome. E Numbers of insertion and deletion on coding sequences (CDS). F Numbers of homologous and heterozygous InDels on CDS. G Length distribution of InDels on genome. H Length distribution of InDels on CDS. Homo, Homozygosity; Het, Heterozygosity

Fig. 2

Principal component analysis (PCA) (A) and phylogenetic tree analysis (B)

Fig. 3

Results of genome-wide selective sweeping. (A) Selective sweeping result of AP vs LP. (B) Selective sweeping result of SP vs LP. (C) Selective sweeping result of AP vs SP. (D) venn diagram of selected genes numbers. (E) Chromosome location of selected genes related to immune, vision, migration, and osmoregulation

Fig. 4

Detection of selected genes related to immune and oxidant stress in livers of AP, LP, and SP. (A-C) activities of GR, SOD, and GSH-Px. (D-H) expression of genes related to immune. The results were showed in means ± SD. Different letters indicate significant difference at P < 0.05

Fig. 5

Detection of selected genes related to vision and rhythm in AP, LP, and SP. (A) eye diameter/head length. (B-C) expression of genes related to vision in eyes. (D) expression of gene related to rhythm in brains. The results were showed in means ± SD. Different letters indicate significant difference at P < 0.05

Fig. 6

Detection of selected genes related to nerve conduction and long-distance migration in AP and LP. (A) expression of genes related to nerve conduction in brains. (B) expression of genes related to long-distance migration in muscles

Fig. 7

Detection of selected genes related to osmoregulation in LP and SP. (A) expression of genes related to osmoregulation in gills. (B) Osmoregulatory mechanisms of LP during hypotonic environment. (C) Osmoregulatory mechanisms of SP during hypertonic environment. Up regulated gene with italic were shown in red and boxed in red. Down regulated gene with italic were shown in green and boxed in green. The red arrows mean promotion, and the green arrows mean inhibition