Adaptability and Evolution of Gobiidae: A Genetic Exploration

Abstract

The Gobiidae family occupy one of the most diverse habitat ranges of all fishes. One key reason for their successful colonization of different habitats is their ability to adapt to different energy demands. This energy requirement is related to the ability of mitochondria in cells to generate energy via oxidative phosphorylation (OXPHOS). Here, we assembled three complete mitochondrial genomes of Rhinogobius shennongensis, Rhinogobius wuyanlingensis, and Chaenogobius annularis. These mitogenomes are circular and include 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region (CR). We used comparative mitochondrial DNA (mtDNA) genome and selection pressure analyses to explore the structure and evolutionary rates of Gobiidae mitogenomics in different environments. The CmC model showed that the ω ratios of all mtDNA PCGs were <1, and that the evolutionary rate of adenosine triphosphate 8 (atp8) was faster in Gobiidae than in other mitochondrial DNA PCGs. We also found evidence of positive selection for several sites of NADH dehydrogenase (nd) 6 and atp8 genes. Thus, divergent mechanisms appear to underlie the evolution of mtDNA PCGs, which might explain the ability of Gobiidae to adapt to diverse environments. Our study provides new insights on the adaptive evolution of Gobiidae mtDNA genome and molecular mechanisms of OXPHOS.

Analysis of the Complete Mitochondrial Genome of Pteronura brasiliensis and Lontra canadensis

“…The overall AT content of the heavy strands of these two mitochondrial genomes was higher than the GC content, indicating AT-rich characteristics. The base compositions were skewed similarly to those of other vertebrate mitochondrial genome sequences [41][42][43]. The AT content was higher than the GC content in most of the mitochondrial genomes of otters (Table 4).…”

Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes

“…For example, the microsatellite characteristics of 19 Gobiidae fish provided powerful support for microsatellite development in Gobiidae [12]. Complete mitogenome assembly in three Gobiidae fish demonstrated that the evolution of mitochondrial genome protein-coding genes (mtDNA PCGs) was crucial to Gobiidae adaptability [13]. Although the Gobiidae family contains more than 2000 species [1], only 18 species' genomes have been published (https://www.ncbi.nlm.nih.gov/genome/?term=Gobiidae, accessed on 7 March 2024).…”

Effect of locomotor preference on the evolution of mitochondrial genes in Bovidae

“…The non-synonymous/synonymous substitution rate (dN/dS) is often used to calculate the evolution of 13 mtDNA PCGs 18 , 19 . Thus, we calculated the rate of evolution of Bovidae mitochondrial genes using dN/dS.…”