The F type mitochondrial genome of hard-shelled mussel: Mytilus coruscus (Mytiloida, Mytilidae)

Nano titanium dioxide alleviates the toxic effects of tris (2-chloropropyl) phosphate on the digestive gland and hemolymph of thick-shell mussel Mytilus coruscus

In the marine environment, nanoparticles play a role in adsorbing and catalytically degrading organic pollutants, thereby mitigating their toxic effects on aquatic organisms. This study aimed to investigate the impact of nano titanium dioxide (nTiO2) and tris (2-chloropropyl) phosphate (TCPP) on the hemolymph and digestive function of the thick-shell mussel Mytilus coruscus. Mussels were divided into a control group, a group exposed to TCPP alone, a group exposed to a combination of TCPP and 0.5 mg/L nTiO2, and a group exposed to a combination of TCPP and 1 mg/L nTiO2. After 14 days of exposure, oxidative stress responses, including superoxide dismutase (SOD) activity and malondialdehyde (MDA) content, immune defense responses, including acid phosphatase (ACP) and alkaline phosphatase (AKP) activities, and gene expression, including HSP70 expression, were measured in the hemolymph and digestive glands of the mussels. Compared to the control group, mussels solely exposed to 100 μg/L TCPP exhibited a significant reduction in SOD activity in the hemolymph. When TCPP was co-exposed with 0.5 mg/L nTiO2, there were significant increases in MDA content and AKP activity in both the digestive gland and hemolymph compared to the control group. Upon co-exposure of TCPP with 1 mg/L nTiO2, MDA content and AKP activity in the digestive gland significantly decreased, while SOD, ACP, and AKP activity in the hemolymph significantly increased and MDA content significantly decreased, returning to the control group levels. Furthermore, in the combined exposure, HSP70 gene expression significantly decreased as the nTiO2 concentration increased from 0.5 mg/L to 1 mg/L. In summary, TCPP impacted the hemolymph and digestive function of mussels, whereas a concentration of 1 mg/L nTiO2 effectively alleviated the toxic effects of TCPP. This study is crucial for assessing the ecological risks of nanoparticles and emerging organic pollutants in marine environments, and provides new insights into the interaction between nTiO2 and TCPP, as well as the influence of nTiO2 concentration on mitigating TCPP toxicity.

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

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08940-8.

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

Two genetically different mitochondrial haplogroups of Brachidontes pharaonis (p-distance 6.8%) have been identified in the Mediterranean Sea. This hinted at a possible presence of doubly uniparental inheritance in this species. To ascertain this possibility, we sequenced two complete mitogenomes of Brachidontes pharaonis mussels and performed a qPCR analysis to measure the relative mitogenome copy numbers of both mtDNAs. Despite the presence of two very similar regions composed entirely of repetitive sequences in the two haplogroups, no recombination between mitogenomes was detected. In heteroplasmic individuals, both mitogenomes were present in the generative tissues of both sexes, which argues against the presence of doubly uniparental inheritance in this species.

The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus

The hard-shelled mussel (Mytilus coruscus) is an economically important shellfish that has been cultivated for the last decade. Due to over-exploitation, most mussel stocks have dramatically declined. Efforts to study this species' natural distribution, genetics, breeding, and cultivation have been hindered by the lack of a high-quality reference genome. To address this, we produced a hybrid high-quality reference genome of M. coruscus using a long-read platform to assemble the genome and short-read, high-quality technology to accurately correct for sequence errors. The genome was assembled into 10,484 scaffolds, a total length of 1.90 Gb, and a scaffold N50 of 898 kb. Ab initio annotation of the M. coruscus genome assembly identified a total of 42,684 genes. This accurate reference genome of M. coruscus provides an essential resource with the advantage of enabling the genome-scale selective breeding of M. coruscus. More importantly, it will also help in deciphering the speciation and local adaptation of the Mytilus species.

A mitochondrial genome phylogeny of Mytilidae (Bivalvia: Mytilida)

The family Mytilidae is a family of bivalve mussels that are distributed worldwide in diverse marine habitats. Within the family, classification systems and phylogenetic relationships among subfamilies remain not yet fully resolved. In this study, we newly determined 9 mitochondrial genome sequences from 7 subfamilies: Bathymodiolus thermophilus (Bathymodiolinae), Modiolus nipponicus (Modiolinae), Lithophaga curta (the first representative of Lithophaginae), Brachidontes mutabilis (Brachidontinae), Mytilisepta virgata (Brachidontinae), Mytilisepta keenae (Brachidontinae), Crenomytilus grayanus (Mytilinae), Gregariella coralliophaga (Crenellinae), and Septifer bilocularis (the first representative of Septiferinae). Phylogenetic trees using maximum likelihood and Bayesian inference methods for 28 mitochondrial genomes (including 19 previously published sequences) showed two major clades with high support values: Clade 1 ((Bathymodiolinae + Modiolinae) + (Lithophaginae + Limnoperninae)) and Clade 2 (((Mytilinae + Crenellinae) + Septiferinae) + Brachidontinae). The position of the genus Lithophaga (representing Lithophaginae) differed from a previously published molecular phylogeny. Divergence time analysis with a molecular clock indicated that lineage splitting among the major subfamilies of Mytilidae (including the habitat transition from marine to freshwater environments by ancestral Limnoperninae) occurred in the Mesozoic period, coinciding with high diversification rates of marine fauna during that time. This is the first mitochondrial genome-based phylogenetic study of the Mytilidae that covers nearly all subfamily members, excluding the subfamily Dacrydiinae.

Transoceanic dispersal of the mussel Mytilus galloprovincialis on Japanese tsunami marine debris: An approach for evaluating rafting of a coastal species at sea

Biofouled debris from the 2011 Great East Japan earthquake and tsunami has landed in the Northeast Pacific and along the Hawaiian Islands since 2012. As of 2017, >630 biofouled debris items with >320 living species of algae, invertebrates, and fish have been examined. The invasive mussel Mytilus galloprovincialis was present on >50% of those items. Size, reproduction, and growth of this filter-feeding species were examined to better understand long-distance rafting of a coastal species. The majority of mussels (79%) had developing or mature gametes, and growth rates averaged 0.075±0.018 SE mm/day. Structural and elemental (barium/calcium) analysis of mussel shells generated estimates of growth in coastal waters (mean=1.3 to 25mm total length), which provides an indication of residence times in waters along North America and the Hawaiian Islands prior to landing. Detailed studies of individual species contribute to our understanding of debris as a transport vector and aid efforts to evaluate potential risks associated with marine debris.

Actively transcribed and expressed atp8 gene in Mytilus edulis mussels

Background

Animal mitochondrial genomes typically encode 37 genes: 13 proteins, 22 tRNAs and two rRNAs. However, many species represent exceptions to that rule. Bivalvia along with Nematoda and Platyhelminthes are often suspected to fully or partially lack the ATP synthase subunit 8 (atp8) gene. This raises the question as to whether they are really lacking this gene or is this maybe an annotation problem? Among bivalves, Mytilus edulis has been inferred to lack an ATP8 gene since the characterization of its mitochondrial genome in 1992. Even though recent bioinformatic analyses suggested that atp8 is present in Mytilus spp., due to high divergence in predicted amino acid sequences, the existence of a functional atp8 gene in this group remains controversial.

Results

Here we demonstrate that M. edulis mitochondrial open reading frames suggested to be atp8 (in male and female mtDNAs) are actively translated proteins. We also provide evidence that both proteins are an integral part of the ATP synthase complex based on in-gel detection of ATP synthase activity and two-dimensional Blue-Native and SDS polyacrylamide electrophoresis.

Conclusion

Many organisms (e.g., Bivalvia along with Nematoda and Platyhelminthes) are considered to be lacking certain mitochondrial genes often only based on poor similarity between protein coding gene sequences in genetically closed species. In some situations, this may lead to the inference that the ATP8 gene is absent, when it is in fact present, but highly divergent. This shows how important complementary role protein-based approaches, such as those in the present study, can provide to bioinformatic, genomic studies (i.e., ability to confirm the presence of a gene).

Mitogenomics of southern hemisphere blue mussels (Bivalvia: Pteriomorphia): Insights into the evolutionary characteristics of the Mytilus edulis complex

Marine blue mussels (Mytilus spp.) are widespread species that exhibit an antitropical distribution with five species occurring in the Northern Hemisphere (M. trossulus, M. edulis, M. galloprovincialis, M. californianus and M. coruscus) and three in the Southern Hemisphere (M. galloprovincialis, M. chilensis and M. platensis). Species limits in this group remain controversial, in particular for those forms that live in South America. Here we investigated structural characteristics of marine mussels mitogenomes, based on published F mtDNA sequences of Northern Hemisphere species and two newly sequenced South American genomes, one from the Atlantic M. platensis and another from the Pacific M. chilensis. These mitogenomes exhibited similar architecture to those of other genomes of Mytilus, including the presence of the Atp8 gene, which is missing in most of the other bivalves. Our evolutionary analysis of mitochondrial genes indicates that purifying selection is the predominant force shaping the evolution of the coding genes. Results of our phylogenetic analyses supported the monophyly of Pteriomorphia and fully resolved the phylogenetic relationships among its five orders. Finally, the low genetic divergence of specimens assigned to M. chilensis and M. platensis suggests that these South American marine mussels represent conspecific variants rather than distinct species.