Mitochondrial genomic analyses provide new insights into the “missing” atp8 and adaptive evolution of Mytilidae

Abstract

Background Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length. Results In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972 bp, 20,482, and 17,786 bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater. Conclusions Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments.

The Complete Mitochondrial Genome of Mytilisepta virgata (Mollusca: Bivalvia), Novel Gene Rearrangements, and the Phylogenetic Relationships of Mytilidae

“…It was beyond the scope of this paper to suggest that further analysis might be needed to produce an affordable taxonomic revision. To our surprise, there were discrepancies between our findings and those of Zhao et al Therefore, further in-depth investigations should be conducted in the future [ 83 ].…”

“…Combosch et al validated the monophyly of the genus Perna and indicated a misidentification in the previous study [ 81 ]. In our analysis, the Mytilisepta was clustered with P. purpuratus , as in previous studies [ 18 , 82 ], but this finding differed from the results presented by Zhao et al [ 83 ]. Moreover, Combosch et al concluded that M. virgata was most closely related to B. exustus by using a five-gene Sanger-based approach [ 81 ].…”

Comprehensive analysis of the complete mitochondrial genomes of three Coptis species (C. chinensis, C. deltoidea and C. omeiensis): the important medicinal plants in China

“…Mitochondrial complex I is the first and largest respiratory complex required in the process of the process of oxidative phosphorylation to generate ATP, which is involved in the mitochondrial electron transport chain and is one of the major production sites of ROS (superoxide anion) ( Huang et al., 2016 ; Subrahmanian et al., 2016 ; Wang et al., 2022a ). Mutations in the members of complex I would change the metabolic capacity which may further affect adaptability of the organism ( Zhao et al., 2022 ).…”

Chromosome-level genome assembly of the disco clam,Ctenoides ales, a first for the bivalve order Limida

“…The only typical metazoan protein coding gene not annotated was atp8, which is commonly absent in bivalve mitogenomes (Serb and Lydeard 2003). However, recent analyses support the presence of atp8 sequences in Pectinidae (Malkócs et al 2022) and Mytilidae (Zhao et al 2022).…”