Abstract
BackgroundCoilia 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.ResultsWhole-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.ConclusionsCombined 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.
Highlights
Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea
Combined to life history of C. nasus populations, our results revealed that the molecular mechanisms of their differences of immune, vision, migration, and osmoregulation
Genome resequencing and mapped on reference genome After filtering adaptors, ambiguous “N” nucleotides, and low-quality sequences, 276.78 G clean reads were generated, and the average sequencing depth was 10 ×. 296.61, 327.20, and 300.66 million clean reads were generated in anadromous population (AP), landlocked population (LP), and sea population (SP), respectively
Summary
Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. The sexually mature fish run thousands of kilometers from marine to river for spawning Another one is the resident population which cannot migrate. The sexually mature fish run thousands of kilometers from marine to river, such as the Yangtze River, to spawn from February [4] During spawning migration, they generally do not feed, but a small part of C. nasus feed [5]. The eggs float down and hatch in the river, and the juveniles migrate the marine [4] Based on their different habitats, one is lake anchovy, resident in the freshwater lake during the entire lifetime. Another one is sea anchovy, resident in marine during the entire lifetime
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