title: Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus).
abstract: The geographic distribution of threeMisgurnusspecies,M. anguillicaudatus,M. bipartitus, andM. mohoity, displays a specific pattern in China, coincident with temperature zones. In this study, we sequenced the transcriptomes of these three species and used the sequences to investigate the lineage-specific adaptations within the genusMisgurnus. In total, 51 orphan genes (19 inM. anguillicaudatus, 18 inM. bipartitus, and 14 inM. mohoity) that may contribute to the species-specific adaptations were identified. An analysis of 1392 one-to-one orthologous genes revealed significantly higher ratios of nonsynonymous-to-synonymous substitutions in theM. mohoitylineage than inM. anguillicaudatus. The genes displaying signatures of positive selection and rapid evolution inMisgurnuswere involved in four function categories, (1) energy metabolism; (2) signal transduction; (3) membrane; and (4) cell proliferation or apoptosis, implying that these candidate genes play critical roles in the thermal adaptation of the fish to their living environments. We also detected more than five positively selected sites in cldn15lb and isca1, which function as important factors in paracellular Na⁺ transport and Fe/S cluster assembly, respectively. Overall, our study provides valuable insights into the adaptive evolution of loaches from different temperature zones in China and is a foundation for future studies to clarify the genetic basis of temperature adaptation in fishes.
authors.affiliation: Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. yishaokui@foxmail.com.|Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. yishaokui@foxmail.com.
authors.forename: Shaokui
authors.initials: S
authors.lastname: Yi
authors.affiliation: Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. saiwang320@163.com.|Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. saiwang320@163.com.
authors.forename: Sai
authors.initials: S
authors.lastname: Wang
authors.affiliation: Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. zhongjia@webmail.hzau.edu.cn.|Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. zhongjia@webmail.hzau.edu.cn.
authors.forename: Jia
authors.initials: J
authors.lastname: Zhong
authors.affiliation: Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. wangwm@mail.hzau.edu.cn.|Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China. wangwm@mail.hzau.edu.cn.
authors.forename: Weimin
authors.initials: W
authors.lastname: Wang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics / Q000502:physiology*; D000818:Animals; D003531:Cypriniformes / Q000145:classification / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D010802:Phylogeny; D013045:Species Specificity; D013696:Temperature
keywords: Misgurnus; adaptive evolution; temperature zone; transcriptome