Comparative analysis of mitochondrial genome of a deep-sea crab Chaceon granulates reveals positive selection and novel genetic features

Phylogenetic Relationships and Adaptation in Deep-Sea Mussels: Insights from Mitochondrial Genomes

“…The ATP synthase F o subunit 6 or complex V drives the last step of oxidative phosphorylation for electron transport chain. Evidence supporting the adaptive evolution of the atp6 gene has been reported in the mitogenome of Glyptothorax macromaculatus [ 47 ], deep-sea fish [ 19 ], and deep-sea polynoids [ 20 ]. Although cob is a conserved gene, it is crucial to the ability of the mitochondria to generate energy through reversible electron transfer from ubiquinol to cytochrome c along with proton translocation.…”

“…In the deep-sea shrimp family Alvinocarididae, the greatest residues of positively selected sites are within nad1-5 [ 39 ], a gene also known to be related to deep-sea hydrothermal vent adaptation. The nad3 and nad5 genes in the mitogenome of the deep-sea crab Chaceon granulates also harbor positively selected residues [ 20 ]. Similarly, 11 residues are considered positively selected in the nad2 and nad4 genes of the deep-sea sea cucumber Benthodytes marianensis [ 39 ].…”

“…Cytochrome c oxidase stimulating the terminal reduction of oxygen and with three mitochondrial PCGs ( cox1 , cox2 , and cox3 ) that encode the catalytic core is an important positive selection target in hypoxia adaptation [ 45 , 46 ]. In deep-sea clams belonging to the family Vesicomyidae, positively selected residues are found in the cox1 and cox3 genes [ 20 ]. The ATP synthase F o subunit 6 or complex V drives the last step of oxidative phosphorylation for electron transport chain.…”

“…Mitogenomes carry useful evolutionary information and have been widely applied in phylogenetic and evolutionary studies of terrestrial and shallow-water organisms, including mussels [ 14 , 15 , 16 , 17 ]. Given that the mitochondria play a key role in the energetic metabolism of metazoans, the hypoxia and high hydrostatic pressure environments in cold seeps and hydrothermal vents could exert selective pressure on the evolution of these energy-producing organelles [ 18 , 19 , 20 , 21 ]. However, only six Bathymodiolinae mitogenomes are currently available, thereby hindering our understanding of their evolution.…”

The complete mitogenome of Phymorhynchus sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep‐sea adaptive evolution of Conoidea

“…Ambiguously aligned regions were removed using Gblocks 0.91b (Talavera & Castresana, 2007) with the default settings. The resulting alignments were concatenated into a single dataset with PhyloSuite (Zhang, Wu, et al, 2020;Zhang, Gao, et al, 2020). The best partition schemes and optimal substitution models were selected by PartitionFinder 2 (Lanfear et al, 2016) with the greedy algorithm and corrected Akaike information criteria (AICc).…”