Genomic basis of evolutionary adaptation in a warm-blooded fish

Abstract

Few fishes have evolved elevated body temperatures compared with ambient temperatures, and only in opah ( Lampris spp) is the entire body affected. To understand the molecular basis of endothermy, we analyzed the opah genome and identified 23 genes with convergent amino acid substitutions across fish, birds, and mammals, including slc8b1 , which encodes the mitochondrial Na + /Ca 2+ exchanger and is essential for heart function and metabolic heat production. Among endothermic fishes, 44 convergent genes with suggestive metabolic functions were identified, such as glrx3 , encoding a crucial protein for hemoglobin maturation. Numerous genes involved in the production and retention of metabolic heat were also found to be under positive selection. Analyses of opah's unique inner-heat-producing pectoral muscle layer (PMI), an evolutionary key innovation, revealed that many proteins were co-opted from dorsal swimming muscles for thermogenesis and oxidative phosphorylation. Thus, the opah genome provides valuable resources and opportunities to uncover the genetic basis of thermal adaptations in fish.

Genomic insights into the adaptive and convergent evolution of Leuciscus waleckii inhabiting extremely alkaline environments

“…A high-quality chromosome-level genome is needed for the downstream analysis of adaptive microevolution 28 . Using the established method, the genome size was evaluated to be approximately 1,125.03 Mb, the heterozygous rate and repeat rate were evaluated as 0.56% and 57.61% respectively by 17-mer analysis (Supplymentary File1: Fig S2 and Table S3) 29 .…”

Temperature acclimation in hot-spring snakes and the convergence of cold response

“…In this study, we identified several REGs, PSGs, and common REGs involved in thermogenesis. Some of these genes, such as TBC1D7 , UTP15 , and GCLC were also identified as PSGs in opah, a warm-blooded fish, 54 suggesting their role in thermal adaptations in vertebrates. However, the function of these genes has been elucidated only in endotherms, remaining unknown in ectothermic reptiles, especially the effects of cold-induced thermogenesis-related genes, and thus require further investigation.…”

Pathways to polar adaptation in fishes revealed by long‐read sequencing

“…In addition to gene copy expansions in vision‐related genes, we also detected a shared signature of selection on vision‐associated genes ( iars2 , nid2a and atxn7 ) in two disparate lineages of polar fish. In mammals, IARS2 has been associated with cataracts (Vona et al, 2018) and it has also been under selection in another ray‐fined, mesopelagic fish, Lamprus guttatus (Wang et al, 2022). The other two genes we identified have been recently linked to degeneration of retinal neurons ( atxn7 , Sun, Chen, & Jin, 2020) and eye development ( nid2a , Carrara, Weaver, Piedade, Vöcking, & Famulski, 2019).…”