Phylogenetic analysis of Brachymystax and Hucho genera—Summary on evolutionary status within the Salmoninae subfamily

Abstract

The family Salmonidae (salmonids) represents an economically and ecologically important freshwater fish group that attracted considerable research attention due their interesting biological features, such as: the tendency to hybridization, a tetraploid origin, high ecological and behavioral diversity as well as wide biographical distribution.The family encompasses more than 200 species distributed over 11 extant genera, which are assigned to three subfamilies, namely: (1) Coregoninae, (2) Thymallinae and (3) Salmoninae (FishBase, 2021).

Chromosome-level genome assembly for Sichuan taimen (hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage

“…The topology inner Salmoninae we inferred was consistent with other studies, the Hucho and Brachymystax formed the ancient branch of the subfamily salmoninae, and constituted the sister group to the genera Salmo, Salvelinus and Oncorhynchus (Crespi and Fulton 2004;Kucinski and Fopp -Bayat 2022). The estimated divergence time based on nuclear genome was similar to the previous researches based on mitochondrial genome (Crête-Lafrenière, et al 2012;Horreo 2017;Kucinski and Fopp-Bayat 2022). The divergence time between the Hucho and Brachymystax was estimated at ~9.28 to ~17.96 Mya, which coincides with the Miocene Climate Optimum (MCO) at 15-18 Mya (Böhme 2003;Sun and Zhang 2008).…”

“…Based on the phylogenetic tree constructed by the orthologous genes, we suggested that Coregoninae and Thymallinae had sister relationship which supported by 100% bootstraps, and was consistent with other trees based on orthologues (Macqueen and Johnston 2014; Robertson, et al 2017), mitochondrial genome (Campbell, et al 2013; Shedko, et al 2013), and ultra-conserved element (Campbell, et al 2020). The topology inner Salmoninae we inferred was consistent with other studies, the Hucho and Brachymystax formed the ancient branch of the subfamily salmoninae, and constituted the sister group to the genera Salmo, Salvelinus and Oncorhynchus (Crespi and Fulton 2004; Kucinski and Fopp - Bayat 2022). The estimated divergence time based on nuclear genome was similar to the previous researches based on mitochondrial genome (Crête-Lafrenière, et al 2012; Horreo 2017; Kucinski and Fopp-Bayat 2022).…”

“…This is consistent with other trees based on orthologues (Macqueen & Johnston, 2014;Robertson et al, 2017), mitochondrial genome (Campbell et al, 2013;Shedko et al, 2013), and ultra-conserved elements (Campbell et al, 2020). The inferred topology within Salmoninae aligns with other studies, with the genera Hucho and Brachymystax forming the ancient branch of the subfamily, constituting a sister group to the genera Salmo, Salvelinus, and Oncorhynchus (Crespi & Fulton, 2004;Kucinski & Fopp-Bayat, 2022). The divergence time between taimen and lenok was estimated at 9.41 to 23.51 Mya, which aligns with previous results based on mitochondria (Kucinski & Fopp-Bayat, 2022), and coincides with the Miocene Climate Optimum (MCO) at 15-18 Mya (Böhme, 2003;Sun & Zhang, 2008).…”

“…A total of 44,120 genes were captured from the Siberia taimen genome, and we identified 4,860 1:1 orthologous genes among the four species. The result of BEAST showed that two taimen species separated at 2.29 Mya (Figure 5B), which was similar to the previous inference (Kucinski & Fopp-Bayat, 2022).…”

“…We identified 36292 orthologous gene families between hucho and the other 9 species, including 479 hucho specific gene families and 267 single copy orthologues. The result of phylogenetic tree based on single copy orthologues revealed that the hucho was a sister group to lenok, and the divergent time estimated by PAML was 12.29 Mya between this two species (Figure 3), which was closed to previous results based on mitochondria (Kucinski and Fopp - Bayat 2022). We generated 916 significant positive expanded gene families in hucho genome, and the results of KEGG pathway showed the enrichments the enrichment of motor and metabolic pathways such as tight junction, adrenergic signaling in cardiomyocytes, glyoxylate and dicarboxylate metabolism and regulation of actin cytoskeleton (Figure S4; Table S7), which was fits with its ferocious hunting habits and large body size.…”