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

Abstract

Mitochondrial genomes (mitogenomes) are an excellent source of information for phylogenetic and evolutionary studies, but their application in marine invertebrates is limited. In the present study, we utilized mitogenomes to elucidate the phylogeny and environmental adaptation in deep-sea mussels (Mytilidae: Bathymodiolinae). We sequenced and assembled seven bathymodioline mitogenomes. A phylogenetic analysis integrating the seven newly assembled and six previously reported bathymodioline mitogenomes revealed that these bathymodiolines are divided into three well-supported clades represented by five Gigantidas species, six Bathymodiolus species, and two “Bathymodiolus” species, respectively. A Common interval Rearrangement Explorer (CREx) analysis revealed a gene order rearrangement in bathymodiolines that is distinct from that in other shallow-water mytilids. The CREx analysis also suggested that reversal, transposition, and tandem duplications with subsequent random gene loss (TDRL) may have been responsible for the evolution of mitochondrial gene orders in bathymodiolines. Moreover, a comparison of the mitogenomes of shallow-water and deep-sea mussels revealed that the latter lineage has experienced relaxed purifying selection, but 16 residues of the atp6, nad4, nad2, cob, nad5, and cox2 genes have underwent positive selection. Overall, this study provides new insights into the phylogenetic relationships and mitogenomic adaptations of deep-sea mussels

Genomic Insights Into Chemosynthetic Symbiosis in a Deep-Sea Hydrothermal Vent Mussel

“…1B and Fig. S3), which is consistent with the result of our previous estimation based on the entire mitogenomes [28]. Gene family analyses revealed the expansion of 17 pfam domains in B. marisindicus (Fig.…”

“…Although often presumed to lack function, pseudogenes may play important biological roles [30], particularly in the regulation of symbiosis [8]. In the present study, 6,026 pseudogenes were identified in the B. marisindicus genome, significantly lower than those reported in A. marissinica (10,211), although the latter has a somewhat higher number of PCGs (28,949) [8]. This larger number of pseudogenes in A. marissinica may be related to the expansion of TEs [8].…”

Contrasting Modes of Mitochondrial Genome Evolution in Sister Taxa of Wood-Eating Marine Bivalves (Teredinidae and Xylophagaidae)

“…Apparent tRNA gene duplications were observed in three of eight putative species examined, involving trnS1, H, D, Y, Q, and M , with putative copy numbers ranging from 2 to 5 per genome. Similarly multiple tRNA gene copies have been reported on other bivalve mitochondrial genomes, for example, in bathymodiolin mussels ( Zhang et al 2021 ). Moreover, in one putative species, represented by xylophagaid specimens E23 and E81, there is an apparent tandem duplication of the rrnS and trnM genes.…”

No evidence of DUI in the Mediterranean alien species Brachidontes pharaonis (P. Fisher, 1870) despite mitochondrial heteroplasmy

“…no Species and references Acc. no Arcuatula senhousia F 41 GU001953 Modiolus nipponicus 94 MK721547 Arcuatula senhousia M 41 GU001954 Modiolus philippinarum 95 KY705073 Bathymodiolus aduloides 96 MT916741 Mytella strigata MT991018 Bathymodiolus azoricus 96 MT916742 Mytilaster solisianus 71 KM655841 Bathymodiolus brooksi 96 MT916743 Mytilisepta keenae 94 MK721542 Bathymodiolus japonicus 97 AP014560 Mytilisepta virgata 94 MK721548 Bathymodiolus marisindicus 96 MT916745 Mytilus californianus F 42 GQ527172 Bathymodiolus manusensis KY270856 Mytilus californianus M 42 GQ527173 Bathymodiolus securiformis NC_039552 Mytilus chilensis 98 KT966847 Bathymodiolus septemdierum 97 AP014562 Mytilus unguiculatus 99 KJ577549 ...…”