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.

Mixed origin of juvenile Atlantic cod (Gadus morhua) along the Swedish west coast

“…Among the annotated outliers, there were also four genes with potential links to migratory behaviour (CACNB3-, OR2K2-, OR56A4-, and SLCO1C1-like). The calcium channel subunit CACNB3 is associated with the annotated outlier locus with the highest F ST between the ecotypes, and has previously been linked with migratory phenotypes in fish (Cao et al ., 2020; Gao et al ., 2021). The two olfactory receptors OR2K2 and OR56A4 are located within a cluster of olfactory genes on chr 16, and olfaction is heavily involved in establishing long-term memory and homing behaviour in fish (Hara, 1994).…”

Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia

“…Current knowledge suggests that the migratory behaviour of fish, such as anadromy in salmonids, results in selective pressure on genomic regions associated with olfaction and sensory perception in general (Gao et al, 2021 ). The above is most likely due to the fact that navigation for natal homing of migrating individuals relies on the detection and processing of environmental stimuli such as odours (Bett & Hinch, 2016 ; Døving et al, 1985 ; Ueda et al, 2016 ; Wisby & Hasler, 1954 ; Yamamoto et al, 2010 ).…”

Characterization of the Ovarian Development and Associated Factors during the Breeding Migration of Coilia nasus in the Yangtze River

“…Xu et al [18] showed that the oocytes in the ovaries of C. nasus at all developmental stages had obvious synchronization and belonged to the type of one-time spawning, and the ovaries could be divided into six developmental stages from I to IV. Recently, more studies have been conducted on the metabolic mechanisms [19], immunity [20,21], energy utilization [22][23][24], and key regulatory pathways in the liver and brain [25] during the reproductive migration of C. nasus, while relatively few studies have been conducted on factors related to ovarian development. In this study, we investigated the changes in the factors related to the reproductive development of C. nasus at the hormone and gene levels.…”