1
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He J, Tao Y, Shao S, Wei H, Yan G, Tang C, Feng J, Li M, Liao Z, Zhang X, Tang C, Buttino I, Wang J, Zhu Z, Yan X. The hidden acceleration pump uncovers the role of shellfish in oceanic carbon sequestration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175699. [PMID: 39179039 DOI: 10.1016/j.scitotenv.2024.175699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 08/02/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Whether shellfish mariculture should be included in the blue carbon profile as a strategy to combat climate change has been controversial. It is highly demanding not only to provide calibration quantitation, but also to provide an ecosystem-based mechanism. In this study, we chose mussel farms as a case study to evaluate their contributions to carbon sinks and their responses to sedimentary carbon fixation and sequestration. First, we quantified the air-sea CO2 flux in the mussel aquacultural zone and observed a weak carbon sink (-0.15 ± 0.07 mmol·m-2·d-1) during spring. Next, by analyzing the carbon composition in the sediment, we recorded a noticeable and unexpected increase in the sedimentary recalcitrant carbon (RC) content in the mussel farming case. To address this surprising sedimentary phenomenon, a long-term indoor experimental test was conducted to distinguish the consequences of mussel engagement with sedimentary RC. Our observational data support the idea that mussel engagement promotes accumulation of RC in sediments by 2.5-fold. Furthermore, the relative intensity of carboxylic-rich alicyclic molecule (CRAM)-like compounds (recalcitrant dissolved organic matter (RDOM)) increased by 451.4 % in the mussel-engaged sedimentary dissolved organic matter (DOM) in comparison to the initial state. Mussel engagement had a significantly positive effect on the abundance of sedimentary carbon-fixing genes. Therefore, we definitively conclude that mussel farming is blue carbon positive and propose a new alternative theory that mussel farming areas may have high carbon sequestration potential via an ecologically integrated "3 M" (microalgae-mussel-microbiota) consortium. The "mussel pump" accelerates carbon sequestration and enhances climate-related ecosystem services.
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Affiliation(s)
- Jianyu He
- Donghai Laboratory, Zhoushan 316021, Zhejiang, China; Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China.
| | - Yulin Tao
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Shuai Shao
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Han Wei
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Guangxiang Yan
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Chunyu Tang
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Jie Feng
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Maosheng Li
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Zhi Liao
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Xiaolin Zhang
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Changsheng Tang
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Isabella Buttino
- Italian Institute for Environmental Protection and Research (ISPRA), Via Vitaliano Brancati 48, 00144 Rome, Italy
| | - Jianxin Wang
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China
| | - Zhuoyi Zhu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Xiaojun Yan
- Laboratory of Marine Biological Resources and Molecular Engineering, Marine Science and Technical College, Zhejiang Ocean University, Zhoushan 316022, Zhejiang, China.
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2
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Kim DU, Kim J, Bae H, Kim T, Lee J, Lee IO, Noh J, Khim JS. Changes in limpet diet according to habitat type. MARINE POLLUTION BULLETIN 2024; 207:116826. [PMID: 39126777 DOI: 10.1016/j.marpolbul.2024.116826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/27/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Limpets are a key taxon regulating the benthic community structure and serving as prey for various predators in rocky shores, however, their role in food web dynamics is still unclear. To determine environmental factors influencing the limpet diet, carbon and nitrogen stable isotopes in limpets and food sources were analyzed on three different coastal habitats. Sediment organic matter contributed the most (86 %) to the limpet diet in bedrocks around tidal flats with abundant sediment supply from the terrestrial matter inflow and the sediment resuspension. Microphytobenthos and macroalgae were the main food sources (57 % and 20 %, respectively) for the limpets around beaches, where benthic flora was abundant. Limpets in bedrocks, erosional habitat, primarily consumed relatively abundant phytoplankton (33 %) and microphytobenthos (28 %). Contrary to previous studies, habitat type, rather than latitude or seawater characteristics, was the most important factor determining the limpet diet. This result also suggests that limpets are non-selective scraper that consume abundant food sources.
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Affiliation(s)
- Dong-U Kim
- School of Earth and Environmental Sciences, Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeongsoo Kim
- Korea Fisheries Resources Agency, Busan 46041, Republic of Korea
| | - Hanna Bae
- Geosystem Research Corporation, Gyeonggi-do 15807, Republic of Korea
| | - Taewoo Kim
- School of Earth and Environmental Sciences, Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongmin Lee
- School of Earth and Environmental Sciences, Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - In Ok Lee
- School of Earth and Environmental Sciences, Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsung Noh
- Department of Environment & Energy, Sejong University, Seoul 05006, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Sciences, Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea.
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3
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Vermeij GJ, DeVries TJ, Griffin M, Nielsen SN, Ochoa D, Rivadeneira MM, Salas‐Gismondi R, Valdovinos F. The temperate marine Peruvian Province: How history accounts for its unusual biota. Ecol Evol 2024; 14:e70048. [PMID: 39041018 PMCID: PMC11260884 DOI: 10.1002/ece3.70048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/27/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
The Peruvian Province, from 6° S in Peru to 42° S in Chile, is a highly productive coastal marine region whose biology and fossil record have long been studied separately but never integrated. To understand how past events and conditions affected today's species composition and interactions, we examined the role of extinction, colonization, geologic changes to explain previously unrecognized peculiar features of the biota and to compare the Peruvian Province's history to that of other climatically similar temperate coasts. We synthesized all available data on the benthic (or benthically feeding) biota, with emphasis on fossilizable taxa, for the interval from the Miocene (23-5.4 Ma) and Pliocene (5.4-2.5 Ma) to the present. We outline the history of ecological guilds including primary producers, herbivores, predators, and suspension-feeders and document patterns of extinction, colonization, and geographic restriction. We identify twelve unusual attributes of the biota, most of which are the result of repeated episodes of extinction. Several guilds present during the Miocene and Pliocene are not represented in the province today, while groups such as kelps and perhaps intertidal predatory sea stars are relative newcomers. Guilds on soft bottoms and in sheltered habitats were severely affected by extinction, whereas those on hard bottoms were most affected by colonists and held their own in diversity. The Peruvian Province has not served as a biogeographic refuge, in contrast to the coasts of Australasia and Argentina, where lineages no longer present in the Peruvian Province survive. The loss of sheltered habitats since the Pliocene explains many of the present-day peculiarities of the biota. The history of the province's biota explains its unique attributes. High productivity, a rich Southern Hemisphere heritage, and colonization from the north account for the present-day composition and unusual characteristics of the biota.
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Affiliation(s)
- Geerat J. Vermeij
- Department of Earth and Planetary SciencesUniversity of California, DavisDavisCaliforniaUSA
| | - Thomas J. DeVries
- Burke Museum of Natural History and CultureUniversity of WashingtonSeattleWashingtonUSA
| | - Miguel Griffin
- División Paleozoología InvertebradosMuseo de La PlataLa PlataArgentina
| | - Sven N. Nielsen
- Instituto de Ciencias de la TierraUniversidad Austral de ChileValdiviaChile
| | - Diana Ochoa
- Centro de Investigación Para el Desarrollo Integral y Sostenible (CIDIS)Universidad Peruana Cayetano HeredioLimaPeru
| | - Marcelo M. Rivadeneira
- Centro de Estudios Avanzados en Zonas ÁridasCoquimboChile
- Departamento de Biologia Marina, Facultad de Ciencias del MarUniversidad Catolica del NorteAntofagastaChile
| | - Rodolfo Salas‐Gismondi
- Departamento de Paleontología de VertebradosMuseo de Historia Natural‐Universidad Nacional Mayor San MarcosLimaPeru
| | - Fernanda Valdovinos
- Department of Environmental Science and PolicyUniversity of California, DavisDavisCaliforniaUSA
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4
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Bramwell G, Schultz AG, Jennings G, Nini UN, Vanbeek C, Biro PA, Beckmann C, Dujon AM, Thomas F, Sherman CDH, Ujvari B. The effect of mitochondrial recombination on fertilization success in blue mussels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169491. [PMID: 38154641 DOI: 10.1016/j.scitotenv.2023.169491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/12/2023] [Accepted: 12/17/2023] [Indexed: 12/30/2023]
Abstract
The presence of doubly uniparental inheritance (DUI) in bivalves represents a unique mode of mitochondrial transmission, whereby paternal (male-transmitted M-type) and maternal (female-transmitted F-type) haplotypes are transmitted to offspring separately. Male embryos retain both haplotypes, but the M-type is selectively removed from females. Due to the presence of heteroplasmy in males, mtDNA can recombine resulting in a 'masculinized' haplotype referred to as Mf-type. While mtDNA recombination is usually rare, it has been recorded in multiple mussel species across the Northern Hemisphere. Given that mitochondria are the powerhouse of the cell, different mtDNA haplotypes may have different selective advantages under diverse environmental conditions. This may be particularly important for sperm fitness and fertilization success. In this study we aimed to i) determine the presence, prevalence of the Mf-type in Australian blue mussels (Mytilus sp.) and ii) investigate the effect of Mf-mtDNA on sperm performance (a fitness correlate). We found a high prevalence of recombined mtDNA (≈35 %) located within the control region of the mitochondrial genome, which occurred only in specimens that contained Southern Hemisphere mtDNA. The presence of two female mitotypes were identified in the studied mussels, one likely originating from the Northern Hemisphere, and the other either representing the endemic M. planulatus species or introduced genotypes from the Southern Hemisphere. Despite having recombination events present in a third of the studied population, analysis of sperm performance indicated no difference in fertilization success related to mitotype.
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Affiliation(s)
- Georgina Bramwell
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Aaron G Schultz
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Geordie Jennings
- Queenscliff Marine Research Facility and Shellfish Hatchery, Victorian Fisheries Australia, Queenscliff, VIC, Australia
| | - Urmi Nishat Nini
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Caitlin Vanbeek
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Peter A Biro
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Christa Beckmann
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia; School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Antoine M Dujon
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia; CREEC, MIVEGEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - Frédéric Thomas
- CREEC, MIVEGEC, UMR IRD 224-CNRS 5290-Université de Montpellier, Montpellier, France
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia; Queenscliff Marine Research Facility and Shellfish Hatchery, Victorian Fisheries Australia, Queenscliff, VIC, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia.
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5
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Yévenes M, Gallardo-Escárate C, Gajardo G. Epigenetic variation mediated by lncRNAs accounts for adaptive genomic differentiation of the endemic blue mussel Mytiluschilensis. Heliyon 2024; 10:e23695. [PMID: 38205306 PMCID: PMC10776947 DOI: 10.1016/j.heliyon.2023.e23695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Epigenetic variation affects gene expression without altering the underlying DNA sequence of genes controlling ecologically relevant phenotypes through different mechanisms, one of which is long non-coding RNAs (lncRNAs). This study identified and evaluated the gene expression of lncRNAs in the gill and mantle tissues of Mytilus chilensis individuals from two ecologically different sites: Cochamó (41°S) and Yaldad (43°S), southern Chile, both impacted by climatic-related conditions and by mussel farming given their use as seedbeds. Sequences identified as lncRNAs exhibited tissue-specific differences, mapping to 3.54 % of the gill transcriptome and 1.96 % of the mantle transcriptome, representing an average of 2.76 % of the whole transcriptome. Using a high fold change value (≥|100|), we identified 43 and 47 differentially expressed lncRNAs (DE-lncRNAs) in the gill and mantle tissue of individuals sampled from Cochamó and 21 and 17 in the gill and mantle tissue of individuals sampled from Yaldad. Location-specific DE-lncRNAs were also detected in Cochamó (65) and Yaldad (94) samples. Via analysis of the differential expression of neighboring protein-coding genes, we identified enriched GO terms related to metabolic, genetic, and environmental information processing and immune system functions, reflecting how the impact of local ecological conditions may influence the M. chilensis (epi)genome expression. These DE-lncRNAs represent complementary biomarkers to DNA sequence variation for maintaining adaptive differences and phenotypic plasticity to cope with natural and human-driven perturbations.
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Affiliation(s)
- Marco Yévenes
- Laboratorio de Genética, Acuicultura y Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Cristian Gallardo-Escárate
- Centro Interdisciplinario para la Investigación en Acuicultura, Universidad de Concepción, Concepción, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura y Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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6
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Zhu L, Li Y, Qiu L, Chen X, Guo B, Li H, Qi P. Screening of genes encoding proteins that interact with Nrf2: Probing a cDNA library from Mytilus coruscus using a yeast two-hybrid system. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109112. [PMID: 37751644 DOI: 10.1016/j.fsi.2023.109112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/08/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
The Nuclear factor Erythroid 2-related factor 2 (Nrf2) is the most important endogenous antioxidant factor in organisms, and it has been demonstrated that it exerts extensive control over the immune response by interacting with crucial innate immunity components directly or indirectly. Although Nrf2 has been widely confirmed to be involved in stress resistance in mammals and some fish, its contribution to mollusks oxidative stress resistance has not frequently been documented. In this investigation, total RNA was taken from the digestive gland of M. coruscus, and a cDNA library was constructed and screened using the GATEWAY recombination technology. The Nrf2 cDNA sequence of M. coruscus was cloned into the pGBKT7 vector to prepare the bait plasmid. Using yeast two-hybrid system, after auxotrophic medium screening, sequencing, and bioinformatics analysis, 13 binding proteins that interacted with Nrf2 were finally identified. They were QM-like protein, 40S ribosomal protein S4 (RPS4), ribosomal protein S2 (RPS2), ribosomal protein L12 (RPL12), EF1-alpha mRNA for elongation factor 1 alpha (eEF1-alpha), ferritin, alpha-amylase, trypsin, vdg3, period clock protein, cyclophilin A isoform 1 (CYP A), serine protease CFSP2, histone variant H2A.Z (H2A.Z). For a better understanding the physiological function of Nrf2 in animals and as a potential target for future research on protein roles in Nrf2 interactions, it is crucial to clarify these protein interactions.
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Affiliation(s)
- Li Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Yaru Li
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Longmei Qiu
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Xinglu Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Baoying Guo
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China
| | - Hongfei Li
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China; Donghai Laboratory, Zhoushan, Zhejiang, 316021, China.
| | - Pengzhi Qi
- National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316004, China; Donghai Laboratory, Zhoushan, Zhejiang, 316021, China.
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7
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Cole M, Artioli Y, Coppock R, Galli G, Saad R, Torres R, Vance T, Yunnie A, Lindeque PK. Mussel power: Scoping a nature-based solution to microplastic debris. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131392. [PMID: 37086672 DOI: 10.1016/j.jhazmat.2023.131392] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/21/2023] [Accepted: 04/08/2023] [Indexed: 05/03/2023]
Abstract
Microplastics are a prolific environmental contaminant. Curbing microplastic pollution requires an array of globally relevant interventions, including source-reduction and curative measures. A novel, nature-based solution to microplastics is proposed, in which mussels are deployed in aquatic ecosystems to act as microplastic biofilters, removing waterborne microplastics and repackaging them into biodeposits that are subsequently captured and removed. Blue mussels (Mytilus edulis) were used to establish the feasibility of such an approach. In the laboratory, mussels were exposed to representative microplastics in a flume tank; at an initial concentration of 1000 microplastics L-1, mussels reduced waterborne microplastic concentrations at an average rate of 40,146 microplastics kg-1 h-1. Mussel faeces sank irrespective of microplastic content, with average sinking velocities of 223-266 m day-1. Modelling predicts ∼3 × 109 mussels deployed on ropes at the mouths of estuaries could remove 4% of waterborne microplastics discharged from rivers. Mussels were successfully deployed in a prototype biodeposit collection system in an urban marina, with 5.0 kg of mussels removing and repackaging 239.9 ± 145.9 microplastics and anthropogenic particles day-1 into their faeces. These results provide impetus for further development of nature-based solutions targeting plastic debris.
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Affiliation(s)
- Matthew Cole
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Yuri Artioli
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Rachel Coppock
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Giovanni Galli
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Radwa Saad
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Ricardo Torres
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | - Thomas Vance
- Plymouth Marine Laboratory Applications Ltd, Prospect Place, Plymouth PL1 3DH, UK
| | - Anna Yunnie
- Plymouth Marine Laboratory Applications Ltd, Prospect Place, Plymouth PL1 3DH, UK
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8
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Gallardo-Escárate C, Valenzuela-Muñoz V, Nuñez-Acuña G, Valenzuela-Miranda D, Tapia FJ, Yévenes M, Gajardo G, Toro JE, Oyarzún PA, Arriagada G, Novoa B, Figueras A, Roberts S, Gerdol M. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes (Basel) 2023; 14:genes14040876. [PMID: 37107634 PMCID: PMC10137854 DOI: 10.3390/genes14040876] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical-chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex.
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Affiliation(s)
| | | | - Gustavo Nuñez-Acuña
- Center for Aquaculture Research, University of Concepción, Concepción 4070386, Chile
| | | | - Fabian J Tapia
- Center for Aquaculture Research, University of Concepción, Concepción 4070386, Chile
| | - Marco Yévenes
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5310230, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5310230, Chile
| | - Jorge E Toro
- Facultad de Ciencias, Instituto de Ciencias Marinas y Limnológicas (ICML), Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Pablo A Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay 2340000, Chile
| | - Gloria Arriagada
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad Andrés Bello, Santiago 8370186, Chile
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), 36208 Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), 36208 Vigo, Spain
| | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, WA 98195, USA
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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9
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Li H, Li C, Ma P, Wang H, Zhang Z. The complete mitochondrial genome of a fouling mussel, Xenostrobus atratus (Mollusca: Mytilidae), and its phylogenetic implication. Mitochondrial DNA B Resour 2023; 8:301-304. [PMID: 36860475 PMCID: PMC9970215 DOI: 10.1080/23802359.2023.2179354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
In this study, we report the female-lineage mitochondrial genome of Xenostrobus atratus for the first time. The circular mitochondrial genome is 14,806 bp in length and contains 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. All genes are encoded on the heavy strand. The genome composition is A + T biased (66.6%), with 25.2% A, 41.4% T, 21.7% G and 11.7% C. A Bayesian inference (BI) phylogenetic tree was constructed based on the mitochondrial genomes of X. atratus and 46 other Mytilidae species. Our results demonstrate that X. atratus and Limnoperna fortunei have distinct lineages, opposing synonymizing Xenostrobus within Limnoperna. According to this study, the validity of the subfamily Limnoperninae and genus Xenostrobus is strongly supported. However, there is still an urgent need for more mitochondrial data to decide to which subfamily X. atratus belongs.
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Affiliation(s)
- Houmei Li
- School of Marine Sciences, Ningbo University, Ningbo, P. R. China,Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo, P. R. China
| | - Peizhen Ma
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Haiyan Wang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Zhen Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China,University of Chinese Academy of Sciences, Beijing, P. R. China,CONTACT Zhen Zhang Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
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Zhao B, Gao S, Zhao M, Lv H, Song J, Wang H, Zeng Q, Liu J. Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae. BMC Genomics 2022; 23:738. [PMID: 36324074 PMCID: PMC9628169 DOI: 10.1186/s12864-022-08940-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08940-8.
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Affiliation(s)
- Baojun Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Shengtao Gao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Mingyang Zhao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hongyu Lv
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Jingyu Song
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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11
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Sánchez-Marín P, Schultze F, Besada V. Use of limpets as alternative to mussels in metal pollution monitoring; application in the Canary Islands. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119614. [PMID: 35709919 DOI: 10.1016/j.envpol.2022.119614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Metal pollution monitoring programs make use of organisms, such as mussels, as biomonitors to evaluate and compare the metal pollution status of coastal areas worldwide. Despite the widespread distribution of mussels of the genus Mytilus, there are places where these organisms are absent or where their abundance is insufficient for biomonitoring purposes, such as in the Canary Islands (Spain). This study considers the use of limpets of the genus Patella as alternative/complementary species in metal pollution monitoring, and compares the bioaccumulation capacity of mussels and limpets collected simultaneously during several sampling campaigns at 11 sampling sites along the continental Spanish Atlantic coastline. Results show that there are some differences in bioaccumulation capacity between limpets and mussels, with limpets showing in average higher concentrations of Cd, Cr, Ni, As and Cu, and lower concentrations of Zn, while concentrations of Hg and Pb were similar for both types of organisms. Significant correlations between metal concentration in mussels and limpets were found for most metals, with the notable exception of Cd, that showed a very different bioaccumulation pattern in both types of organisms. Limpet to mussel metal concentration ratios were derived that can be used to compare the results of metal biomonitoring using either limpets or mussels, and limpets were successfully used in a monitoring survey in the Canary Islands.
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Affiliation(s)
- Paula Sánchez-Marín
- Centro Oceanográfico de Vigo (IEO-CSIC), Subida a Radio Faro, 50, 36390, Vigo, Spain.
| | - Fernando Schultze
- Centro Oceanográfico de Vigo (IEO-CSIC), Subida a Radio Faro, 50, 36390, Vigo, Spain
| | - Victoria Besada
- Centro Oceanográfico de Vigo (IEO-CSIC), Subida a Radio Faro, 50, 36390, Vigo, Spain
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12
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Stable isotope and trace element analysis for tracing the geographical origin of the Mediterranean mussel (Mytilus galloprovincialis) in food authentication. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Adaptive mitochondrial genome functioning in ecologically different farm-impacted natural seedbeds of the endemic blue mussel Mytilus chilensis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100955. [PMID: 35065314 DOI: 10.1016/j.cbd.2021.100955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
We assessed the adaptive contribution of the mitochondrial genes involved with the respiratory chain and oxidative phosphorylation of the blue mussel Mytilus chilensis, a native and heavily exploited species in the inner sea of Chiloé Island, southern Chile. The assembled mitochondrial transcriptome of individuals from two ecologically different farm-impacted natural seedbeds, Cochamó (41°S) and Yaldad (42°S), represented about 4.5% of the whole de novo transcriptome of the species and showed location and tissue (gills, mantle) specific expression differences in 13 protein-coding mitochondrial genes. The RNA-Seq analysis detected differences in the number of up-regulated mitogenes between individuals from Cochamó (7) and Yaldad (11), some being tissue-specific (ND4L and COX2). However, the analysis did not detect transcripts-per-million (TPM = 0) of ND2 and ND5 in gills and ATP6 in mantle samples from Cochamó. Likewise, for ND6 and ATP8 in any sample. Several monomorphic location-specific mitochondrial genetic variants were detected in samples from Cochamó (78) and Yaldad (207), representing standing genetic variability to optimize mitochondrial functioning under local habitats. Overall, these mitochondrial transcriptomic differences reflect the impact of environmental conditions on the mitochondrial genome functioning and offer new markers to assess the effects on mussel fitness of habitat translocations, a routine industry practice. Likewise, these mitochondrial markers should help monitor and maintain adaptive population differences in this keystone and heavily exploited native species.
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14
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Giusti A, Malloggi C, Tosi F, Boldini P, Larraín Barth MA, Araneda C, Arcangeli G, Armani A. Mislabeling assessment and species identification by PCR-RFLP of mussel-based products (Mytilus spp.) sold on the Italian market. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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15
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Falfushynska H, Sokolov EP, Fisch K, Gazie H, Schulz-Bull DE, Sokolova IM. Biomarker-based assessment of sublethal toxicity of organic UV filters (ensulizole and octocrylene) in a sentinel marine bivalve Mytilus edulis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149171. [PMID: 34329935 DOI: 10.1016/j.scitotenv.2021.149171] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
The global occurrence of organic UV filters in the marine environment is of increasing ecotoxicological concern. Here we assessed the toxicity of UV filters ensulizole and octocrylene in the blue mussels Mytilus edulis exposed to 10 or 100 μg l-1 of octocrylene and ensulizole for two weeks. An integrated battery of biochemical and molecular biomarkers related to xenobiotics metabolism and cellular toxicity (including oxidative stress, DNA damage, apoptosis, autophagy and inflammation) was used to assess the toxicity of these UV filters in the mussels. Octocrylene (but not ensulizole) accumulated in the mussel tissues during the waterborne exposures. Both studied UV filters induced sublethal toxic effects in M. edulis at the investigated concentrations. These effects involved induction of oxidative stress, genotoxicity (indicated by upregulation of DNA damage sensing and repair markers), upregulation of apoptosis and inflammation, and dysregulation of the xenobiotic biotransformation system. Octocrylene induced cellular stress in a concentration-dependent manner, whereas ensulizole appeared to be more toxic at the lower (10 μg l-1) studied concentration than at 100 μg l-1. The different concentration-dependence of sublethal effects and distinct toxicological profiles of ensulizole and octocrylene show that the environmental toxicity is not directly related to lipophilicity and bioaccumulation potential of these UV filters and demonstrate the importance of using bioassays for toxicity assessment of emerging pollutants in coastal marine ecosystems.
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Affiliation(s)
- Halina Falfushynska
- Department of Marine Biology, Institute for Biological Sciences, University of Rostock, Rostock, Germany; Department of Human Health, Physical Rehabilitation and Vital Activity, Ternopil V. Hnatiuk National Pedagogical University, Ternopil, Ukraine
| | - Eugene P Sokolov
- Leibniz Institute for Baltic Sea Research, Leibniz Science Campus Phosphorus Research, Warnemünde, Rostock, Germany
| | - Kathrin Fisch
- Department Marine Chemistry, Leibniz-Institute for Baltic Sea Research Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Hatem Gazie
- Department Marine Chemistry, Leibniz-Institute for Baltic Sea Research Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Detlef E Schulz-Bull
- Department Marine Chemistry, Leibniz-Institute for Baltic Sea Research Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Inna M Sokolova
- Department of Marine Biology, Institute for Biological Sciences, University of Rostock, Rostock, Germany; Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany.
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16
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Li J, Wang Z, Rotchell JM, Shen X, Li Q, Zhu J. Where are we? Towards an understanding of the selective accumulation of microplastics in mussels. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117543. [PMID: 34119866 DOI: 10.1016/j.envpol.2021.117543] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Mussels are suggested as bioindicators of marine microplastic pollution. However, they are selective in regards to accumulation of microplastics. To make studies more targeted and comparable, ultimately helping to determine the suitability of the mussel as a bioindicator species for microplastic exposure, we review the published literature that has directly or indirectly demonstrated particle selection in mussels. The reported difference between microplastic levels in mussel tissues and environmental matrices provides evidence for their selective uptake characteristics. Both the organ-specific fate characteristics of microplastics, and the different movement patterns of microplastics in the same organ, show that selective translocation processes take place. The selective elimination is reflected in multiple aspects which include (1) the different characteristics of microplastics in excretion and mussel body; (2) the different retention time of various microplastics in mussels; and (3) the tissue-specific change in the numbers of microplastics during the depuration process. This selectivity is affected by the characteristics of the microplastics, the environmental, or laboratory exposure concentrations, feeding status, and other factors. There are still many research gaps and contradictory viewpoints in this field due to this complexity. The current methodology needs improvement and a breakthrough in standardization.
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Affiliation(s)
- Jiana Li
- College of Oceanography, Hohai University, Nanjing, 210098, China.
| | - Zhenglu Wang
- College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Jeanette M Rotchell
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - Xiaoteng Shen
- College of Harbour, Coastal and Offshore Engineering, Hohai University, Nanjing, 210098, China
| | - Qipei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Jingmin Zhu
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, College of Marine Sciences, Beibu Gulf University, Qinzhou, 535011, China
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17
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Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation. PLoS One 2021; 16:e0256961. [PMID: 34473778 PMCID: PMC8412288 DOI: 10.1371/journal.pone.0256961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Smooth-shelled blue mussels, Mytilus spp., have a worldwide antitropical distribution and are ecologically and economically important. Mussels of the Mytilus edulis species complex have been the focus of numerous taxonomic and biogeographical studies, in particular in the Northern hemisphere, but the taxonomic classification of mussels from South America remains unclear. The present study analysed 348 mussels from 20 sites in Argentina, Chile, Uruguay and the Falkland Islands on the Atlantic and Pacific coasts of South America. We sequenced two mitochondrial locus, Cytochrome c Oxidase subunit I (625 bp) and 16S rDNA (443 bp), and one nuclear gene, ribosomal 18S rDNA (1770 bp). Mitochondrial and nuclear loci were analysed separately and in combination using maximum likelihood and Bayesian inference methods to identify the combination of the most informative dataset and model. Species delimitation using five different models (GMYC single, bGMYC, PTP, bPTP and BPP) revealed that the Mytilus edulis complex in South America is represented by three species: native M. chilensis, M. edulis, and introduced Northern Hemisphere M. galloprovincialis. However, all models failed to delimit the putative species Mytilus platensis. In contrast, however, broad spatial scale genetic structure in South America using Geneland software to analyse COI sequence variation revealed a group of native mussels (putatively M. platensis) in central Argentina and the Falkland Islands. We discuss the scope of species delimitation methods and the use of nuclear and mitochondrial genetic data to the recognition of species within the Mytilus edulis complex at regional and global scales.
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18
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Yévenes M, Núñez-Acuña G, Gallardo-Escárate C, Gajardo G. Adaptive Differences in Gene Expression in Farm-Impacted Seedbeds of the Native Blue Mussel Mytilus chilensis. Front Genet 2021; 12:666539. [PMID: 34093658 PMCID: PMC8174845 DOI: 10.3389/fgene.2021.666539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023] Open
Abstract
The study of adaptive population differences is relevant for evolutionary biology, as it evidences the power of selective local forces relative to gene flow in maintaining adaptive phenotypes and their underlying genetic determinants. However, human-mediated hybridization through habitat translocations, a common and recurrent aquaculture practice where hybrids could eventually replace local genotypes, risk populations' ability to cope with perturbations. The endemic marine mussel Mytilus chilensis supports a booming farming industry in the inner sea of Chiloé Island, southern Chile, which entirely relies on artificially collected seeds from natural beds that are translocated to ecologically different fattening centers. A matter of concern is how farm-impacted seedbeds will potentially cope with environmental shifts and anthropogenic perturbations. This study provides the first de novo transcriptome of M. chilensis; assembled from tissue samples of mantles and gills of individuals collected in ecologically different farm-impacted seedbeds, Cochamó (41°S) and Yaldad (43°S). Both locations and tissue samples differentially expressed transcripts (DETs) in candidate adaptive genes controlling multiple fitness traits, involved with metabolism, genetic and environmental information processing, and cellular processes. From 189,743 consensus contigs assembled: 1,716 (Bonferroni p value ≤ 0.05) were DETs detected in different tissues of samples from different locations, 210 of them (fold change ≥ | 100|) in the same tissue of samples from a different location, and 665 (fold change ≥ | 4|) regardless of the tissue in samples from a different location. Site-specific DETs in Cochamó (169) and Yaldad (150) in candidate genes controlling tolerance to temperature and salinity shifts, and biomineralization exhibit a high number of nucleotide genetic variants with regular occurrence (frequency > 99%). This novel M. chilensis transcriptome should help assessing and monitoring the impact of translocations in wild and farm-impacted mussel beds in Chiloé Island. At the same time, it would help designing effective managing practices for conservation, and translocation traceability.
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Affiliation(s)
- Marco Yévenes
- Programa de Doctorado en Ciencias, Mención Conservación y Manejo de Recursos Naturales, Universidad de Los Lagos, Osorno, Chile
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Gustavo Núñez-Acuña
- Laboratorio de Biotecnología y Genómica Acuícola, Centro Interdisciplinario para la Investigación en Acuicultura, Universidad de Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratorio de Biotecnología y Genómica Acuícola, Centro Interdisciplinario para la Investigación en Acuicultura, Universidad de Concepción, Concepción, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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19
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Iritani R, Noriyuki S. Reproductive interference hampers species coexistence despite conspecific sperm precedence. Ecol Evol 2021; 11:1957-1969. [PMID: 33717434 PMCID: PMC7920778 DOI: 10.1002/ece3.7166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
Negative interspecific mating interactions, known as reproductive interference, can hamper species coexistence in a local patch and promote niche partitioning or geographical segregation of closely related species. Conspecific sperm precedence (CSP), which occurs when females that have mated with both conspecific and heterospecific males preferentially use conspecific sperm for fertilization, might contribute to species coexistence by mitigating the costs of interspecific mating and hybridization. We discussed whether two species exhibiting CSP can coexist in a local environment in the presence of reproductive interference. First, using a behaviorally explicit mathematical model, we demonstrated that two species characterized by negative mating interactions are unlikely to coexist because the costs of reproductive interference, such as loss of mating opportunity with conspecific partners, are inevitably incurred when individuals of both species are present. Second, we experimentally examined differences in mating activity and preference in two Harmonia ladybird species known to exhibit CSP. These behavioral differences may lead to local extinction of H. yedoensis because of reproductive interference by H. axyridis. This prediction is consistent with field observations that H. axyridis uses various food sources and habitats whereas H. yedoensis is confined to a less preferred prey item and a pine tree habitat. Finally, by a comparative approach, we observed that niche partitioning or parapatric distribution, but not sympatric coexistence in the same habitat, is maintained between species with CSP belonging to a wide range of taxa, including vertebrates and invertebrates living in aquatic or terrestrial environments. Taken together, it is possible that reproductive interference may destabilize local coexistence even in closely related species that exhibit CSP.
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Affiliation(s)
| | - Suzuki Noriyuki
- Faculty of Agriculture and Marine ScienceKochi UniversityKochiJapan
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20
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Mussels (Mytilus spp.) products authentication: A case study on the Italian market confirms issues in species identification and arises concern on commercial names attribution. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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21
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Anand PP, Vardhanan YS. Computational modelling of wet adhesive mussel foot proteins (Bivalvia): Insights into the evolutionary convolution in diverse perspectives. Sci Rep 2020; 10:2612. [PMID: 32054875 PMCID: PMC7018726 DOI: 10.1038/s41598-020-59169-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/24/2020] [Indexed: 11/25/2022] Open
Abstract
Underwater adhesion in mussels (Bivalvia) is an extreme adaptation to achieve robust and firm wet adhesion in the freshwater/brackish/ocean, which biochemically shaped through millions of years. The protein-based adhesion has huge prospective in various fields like industry, medical, etc. Currently, no comprehensive records related to the systematic documentation of structural and functional properties of Mussel foot proteins (Mfps). In this study, we identified the nine species of bivalves in which the complete sequence of at least one adhesive protein is known. The insilico characterization revealed the specific physio-chemical structural and functional characters of each Mfps. The evolutionary analyses of selected bivalves are mainly based on Mfps, Mitogenome, and TimeTree. The outcome of the works has great applications for designing biomimetic materials in future.
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Affiliation(s)
- P P Anand
- Biochemistry & Toxicology Division, Department of Zoology, University of Calicut, Kerala, 673 635, India.
| | - Y Shibu Vardhanan
- Biochemistry & Toxicology Division, Department of Zoology, University of Calicut, Kerala, 673 635, India.
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22
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Charles M, Trancart S, Oden E, Houssin M. Experimental infection of Mytilus edulis by two Vibrio splendidus-related strains: Determination of pathogenicity level of strains and influence of the origin and annual cycle of mussels on their sensitivity. JOURNAL OF FISH DISEASES 2020; 43:9-21. [PMID: 31659783 DOI: 10.1111/jfd.13094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
This study aimed at assessing the pathogenicity of two Vibrio splendidus-related species and evaluating the influence of the origin and annual life cycle of mussels on their sensitivity during a bacterial challenge. Thus, in vivo infection assays were made with Vibrio crassostreae 7T4_12 and Vibrio splendidus 3G1_6, over, respectively, thirteen and 9 months, on adult blue mussels from five recruitment areas in France. Two bacterial concentrations were tested: one consistent with the loads of Vibrio spp. in environment and mussel tissues (~105 CFU/ml) and another one much higher (~108 CFU/ml). The tested environmental concentration has no pathogenic effect whatever the time of year, the strain used and the origin of mussels. However, at the highest concentration, a pathogenic effect was observed only at specific moments, and one of the origins appeared to be more resistant. The physiological state of mussels-depending on the time of year-seemed significant in mussels' sensitivity, as their recruitment origin. This study is the first to test the pathogenicity of V. splendidus-related strains at concentrations close to what is found in the wild, over the annual cycle of mussels, and considering their origin.
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Affiliation(s)
- Maud Charles
- UMR BOREA, CNRS-7208, IRD-207, MNHN, UPMC, UCN, Esplanade de la Paix, Normandie Université, Université de Caen Normandie, Caen, France
- LABÉO Frank Duncombe, Caen, France
| | | | | | - Maryline Houssin
- UMR BOREA, CNRS-7208, IRD-207, MNHN, UPMC, UCN, Esplanade de la Paix, Normandie Université, Université de Caen Normandie, Caen, France
- LABÉO Frank Duncombe, Caen, France
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A mitochondrial genome phylogeny of Mytilidae (Bivalvia: Mytilida). Mol Phylogenet Evol 2019; 139:106533. [PMID: 31185299 DOI: 10.1016/j.ympev.2019.106533] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 11/22/2022]
Abstract
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.
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Malachowicz M, Wenne R. Mantle transcriptome sequencing of Mytilus spp. and identification of putative biomineralization genes. PeerJ 2019; 6:e6245. [PMID: 30723611 PMCID: PMC6359903 DOI: 10.7717/peerj.6245] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/09/2018] [Indexed: 12/16/2022] Open
Abstract
In molluscs, the shell secreted by mantle tissue during the biomineralization process is the first barrier against predators and mechanical damage. Changing environmental conditions, such as ocean acidification, influence shell strength and thus protection of the soft body within. Mussels are marine bivalves with important commercial and ecological value worldwide. Despite this importance, the proteins involved in the biomineralization and pigmentation processes in Mytilus spp. remain unclear, as does taxonomy of Mytilus taxa, though there have been many molecular studies. To further understanding in these areas, this study aimed to characterize and compare mantle transcriptomes of four mussel taxa using next generation sequencing. Mussels representing four taxa, were collected from several localities and RNA from mantle tissue was extracted. RNA sequences obtained were assembled, annotated and potential molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were identified. Candidate contigs putatively related to biomineralization and pigmentation processes were then selected and several transcripts were chosen for phylogenetic analyses from the Bivalvia class. Transcriptome comparisons between Mytilus taxa, including gene ontology (GO) enrichment analysis and orthologues identification were performed. Of assembled contigs, 46.57%, 37.28% and 17.53% were annotated using NCBI NR, GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Potential SSRs (483) and SNPs (1,497) were identified. Results presented a total of 1,292 contigs putatively involved in biomineralization and melanogenesis. Phylogenetic analyses of α-carbonic anhydrase, chitinase and tyrosinase revealed complex evolutionary history and diversity of these genes, which may be a result of duplication events or adaptation to different environments in mussels and other bivalves. Enrichment analyses revealed GO terms associated with pH and thermal response in Mytilus edulis from the North Sea and M. galloprovincialis from the Mediterranean Sea. The phylogenetic analysis within the genus Mytilus revealed M. californianus and M. coruscus to be genetically more distant from the other taxa: M. trossulus, M. edulis, M. chilensis and M. galloprovincialis. This work represents the first mantle transcriptome comparison between Mytilus taxa and provides contigs putatively involved in biomineralization.
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Affiliation(s)
| | - Roman Wenne
- Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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25
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Oh R, Lee MJ, Kim YO, Nam BH, Kong HJ, Kim JW, Park JY, Seo JK, Kim DG. Purification and characterization of an antimicrobial peptide mytichitin-chitin binding domain from the hard-shelled mussel, Mytilus coruscus. FISH & SHELLFISH IMMUNOLOGY 2018; 83:425-435. [PMID: 30195913 DOI: 10.1016/j.fsi.2018.09.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 06/08/2023]
Abstract
An antimicrobial peptide with 55 amino acid residues was purified by C18 reversed-phase high-performance liquid chromatography (HPLC) from foot extract of the hard-shelled mussel, Mytilus coruscus. This peptide showed strong antimicrobial activity against Gram-positive and Gram-negative bacteria, as well as fungi. The purified peptide was determined to have a molecular mass of 6202 Da by matrix-assisted laser desorption/ionization time-of-flight mass spectrophotometry (MALDI-TOF/MS). The identified 20-amino acid sequence of the purified peak by Edman degradation shared 100% identity with the N-terminal regions of mytichitin-1, mytichitin-2, mytichitin-3, mytichitin-4, mytichitin-5, and chitinase-like protein-1, and so was named mytichitin-CBD. The cDNA of mytichitin-CBD was cloned and sequenced by rapid amplification of cDNA ends (RACE). The mRNA transcripts were mainly detected in foot tissue, and they were up-regulated and peaked at 4 h after bacterial infection. We constructed and expressed recombinant mytichitin-CBD protein which displayed antimicrobial activity against Gram-negative bacteria Gram-positive bacteria and the fungus as well as anti-parasitic activity against scuticociliates. The results of this study demonstrate that the peptide isolated from M. coruscus is related to the innate immune system of this marine invertebrate and is a possible alternative to antibiotics.
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Affiliation(s)
- Ryunkyoung Oh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Min Jeong Lee
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Ju-Won Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Jung-Kil Seo
- Department of Food Science and Biotechnology, Kunsan National University, Kunsan, 54150, Republic of Korea.
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea.
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Plazzi F, Passamonti M. Footprints of unconventional mitochondrial inheritance in bivalve phylogeny: Signatures of positive selection on clades with doubly uniparental inheritance. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12253] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
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Illesca A, Oyarzún PA, Toro JE, Gardner JPA. Morphometric variability of smooth-shelled blue mussels from the Pacific coast of South America. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Alex Illesca
- Instituto de Ciencias Marinas y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Independencia, Valdivia, Chile
| | - Pablo A Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ) Universidad Andrés Bello, Quintay, Chile
| | - Jorge E Toro
- Instituto de Ciencias Marinas y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Independencia, Valdivia, Chile
| | - Jonathan P A Gardner
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Lubośny M, Przyłucka A, Śmietanka B, Breton S, Burzyński A. Actively transcribed and expressed atp8 gene in Mytilus edulis mussels. PeerJ 2018; 6:e4897. [PMID: 29900071 PMCID: PMC5995098 DOI: 10.7717/peerj.4897] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/11/2018] [Indexed: 01/08/2023] Open
Abstract
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).
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Aleksandra Przyłucka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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Zbawicka M, Trucco MI, Wenne R. Single nucleotide polymorphisms in native South American Atlantic coast populations of smooth shelled mussels: hybridization with invasive European Mytilus galloprovincialis. Genet Sel Evol 2018; 50:5. [PMID: 29471805 PMCID: PMC5824471 DOI: 10.1186/s12711-018-0376-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Throughout the world, harvesting of mussels Mytilus spp. is based on the exploitation of natural populations and aquaculture. Aquaculture activities include transfers of spat and live adult mussels between various geographic locations, which may result in large-scale changes in the world distribution of Mytilus taxa. Mytilus taxa are morphologically similar and difficult to distinguish. In spite of much research on taxonomy, evolution and geographic distribution, the native Mytilus taxa of the Southern Hemisphere are poorly understood. Recently, single nucleotide polymorphisms (SNPs) have been used to clarify the taxonomic status of populations of smooth shelled mussels from the Pacific coast of South America. In this paper, we used a set of SNPs to characterize, for the first time, populations of smooth shelled mussels Mytilus from the Atlantic coast of South America. RESULTS Mytilus spp. samples were collected from eastern South America. Six reference samples from the Northern Hemisphere were used: Mytilus edulis from USA and Northern Ireland, Mytilus trossulus from Canada, and Mytilus galloprovincialis from Spain and Italy. Two other reference samples from the Southern Hemisphere were included: M. galloprovincialis from New Zealand and Mytilus chilensis from Chile. Fifty-five SNPs were successfully genotyped, of which 51 were polymorphic. Population genetic analyses using the STRUCTURE program revealed the clustering of eight populations from Argentina (Mytilus platensis) and the clustering of the sample from Ushuaia with M. chilensis from Chile. All individuals in the Puerto Madryn (Argentina) sample were identified as M. platensis × M. galloprovincialis F2 (88.89%) hybrids, except one that was classified as Mediterranean M. galloprovincialis. No F1 hybrids were observed. CONCLUSIONS We demonstrate that M. platensis (or Mytilus edulis platensis) and M. chilensis are distinct native taxa in South America, which indicates that the evolutionary histories of Mytilus taxa along the Atlantic and Pacific coasts differ. M. platensis is endangered by hybridization with M. galloprovincialis that was introduced from Europe into the Puerto Madryn area in Argentina, presumably by accidental introduction via ship traffic. We confirm the occurrence of a native M. chilensis population in southern Argentina on the coast of Patagonia.
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Affiliation(s)
- Małgorzata Zbawicka
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland
| | - María I Trucco
- Instituto Nacional de Investigación y Desarrollo Pesquero, Paseo Victoria Ocampo No. 1, B7602HSA, Mar Del Plata, Buenos Aires, Argentina
| | - Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland.
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Larraín MA, Zbawicka M, Araneda C, Gardner JPA, Wenne R. Native and invasive taxa on the Pacific coast of South America: Impacts on aquaculture, traceability and biodiversity of blue mussels (Mytilusspp.). Evol Appl 2017. [DOI: 10.1111/eva.12553] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Maria A. Larraín
- Departamento de Ciencia de los Alimentos y Tecnología Química; Facultad de Ciencias Químicas y Farmacéuticas; Universidad de Chile; Santiago Chile
| | | | - Cristian Araneda
- Departamento de Producción Animal; Facultad de Ciencias Agronómicas; Universidad de Chile; Santiago Chile
| | - Jonathan P. A. Gardner
- School of Biological Sciences; Victoria University of Wellington; Wellington New Zealand
| | - Roman Wenne
- Institute of Oceanology; Polish Academy of Sciences; Sopot Poland
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31
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Sun S, Li Q, Kong L, Yu H. Multiple reversals of strand asymmetry in molluscs mitochondrial genomes, and consequences for phylogenetic inferences. Mol Phylogenet Evol 2017; 118:222-231. [PMID: 29038046 DOI: 10.1016/j.ympev.2017.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 10/08/2017] [Accepted: 10/12/2017] [Indexed: 01/05/2023]
Abstract
Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. The strand-specific bias in the nucleotide composition of the mtDNA has been known to be highly problematic for phylogenetic analyses. Here, the strand asymmetry was compared across 140 mollusc species and analyzed for a mtDNA fragment including twelve protein-coding genes. The analyses show that almost all species in Gastropoda (except Heterobranchia) and all species in Bivalvia present reversals of strand bias. The skew values on individual genes for all codon positions (P123), third codon positions (P3), and fourfold redundant third codon positions (P4FD) indicated that CG skews are the best indicators of strand asymmetry. The differences in the patterns of strand asymmetry significantly influenced the amino acid composition of the encoded proteins. These biases are most striking for the amino acids Valine, Cysteine, Asparagine and Threonines, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. Molluscs with strong variability of genome architectures (ARs) are usually characterized by a reversal of the usual strand bias. Phylogenetic analyses show that reversals of asymmetric mutational constraints have consequences on the phylogenetic inferences, as taxa characterized by reverse strand bias (Heterobranchia and Bivalvia) tend to group together due to long-branch attraction (LBA) artifacts. Neutral Transitions Excluded (NTE) model did not overcome the problem of heterogeneous biases present in molluscs mt genomes, suggested it may not be appropriate for molluscs mt genome data. Further refinement phylogenetic models may help us better understand internal relationships among these diverse organisms.
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Affiliation(s)
- Shao'e Sun
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, China.
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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32
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Chrzanowska-Lightowlers Z, Rorbach J, Minczuk M. Human mitochondrial ribosomes can switch structural tRNAs - but when and why? RNA Biol 2017; 14:1668-1671. [PMID: 28786741 PMCID: PMC5731804 DOI: 10.1080/15476286.2017.1356551] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
High resolution cryoEM of mammalian mitoribosomes revealed the unexpected presence of mitochondrially encoded tRNA as a structural component of mitochondrial large ribosomal subunit (mt-LSU). Our previously published data identified that only mitochondrial (mt-) tRNAPhe and mt-tRNAVal can be incorporated into mammalian mt-LSU and within an organism there is no evidence of tissue specific variation. When mt-tRNAVal is limiting, human mitoribosomes can integrate mt-tRNAPhe instead to generate a translationally competent monosome. Here we discuss the possible reasons for and consequences of the observed plasticity of the structural mt-tRNA integration. We also indicate potential direction for further research that could help our understanding of the mechanistic and evolutionary aspects of this unprecedented system.
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Affiliation(s)
- Zofia Chrzanowska-Lightowlers
- a The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience , Newcastle University , Newcastle upon Tyne , England , UK
| | - Joanna Rorbach
- b Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Retzius väg 8, Stockholm , Sweden
| | - Michal Minczuk
- c MRC Mitochondrial Biology Unit , Wellcome Trust/MRC Building, Hills Road, Cambridge, England , UK
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García-Souto D, Sumner-Hempel A, Fervenza S, Pérez-García C, Torreiro A, González-Romero R, Eirín-López JM, Morán P, Pasantes JJ. Detection of invasive and cryptic species in marine mussels (Bivalvia, Mytilidae): A chromosomal perspective. J Nat Conserv 2017. [DOI: 10.1016/j.jnc.2017.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Beyer J, Green NW, Brooks S, Allan IJ, Ruus A, Gomes T, Bråte ILN, Schøyen M. Blue mussels (Mytilus edulis spp.) as sentinel organisms in coastal pollution monitoring: A review. MARINE ENVIRONMENTAL RESEARCH 2017; 130:338-365. [PMID: 28802590 DOI: 10.1016/j.marenvres.2017.07.024] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 05/16/2023]
Abstract
The blue mussel (Mytilus spp.) is widely used as a bioindicator for monitoring of coastal water pollution (mussel watch programs). Herein we provide a review of this study field with emphasis on: the suitability of Mytilus spp. as environmental sentinels; uptake and bioaccumulation patterns of key pollutant classes; the use of Mytilus spp. in mussel watch programs; recent trends in Norwegian mussel monitoring; environmental quality standards and background concentrations of key contaminants; pollutant effect biomarkers; confounding factors; particulate contaminants (microplastics, engineered nanomaterials); climate change; harmonization of monitoring procedures; and the use of deployed mussels (transplant caging) in pollution monitoring. Lastly, the overall state of the art of blue mussel pollution monitoring is discussed and some important issues for future research and development are highlighted.
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Affiliation(s)
- Jonny Beyer
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway.
| | - Norman W Green
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Steven Brooks
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Ian J Allan
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Anders Ruus
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway; University of Oslo, Department of Biosciences, NO-0316, Oslo, Norway
| | - Tânia Gomes
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Inger Lise N Bråte
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Merete Schøyen
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
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Plazzi F, Puccio G, Passamonti M. Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia. Genome Biol Evol 2016; 8:2544-64. [PMID: 27503296 PMCID: PMC5010914 DOI: 10.1093/gbe/evw187] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2016] [Indexed: 12/28/2022] Open
Abstract
Despite the figure of complete bivalve mitochondrial genomes keeps growing, an assessment of the general features of these genomes in a phylogenetic framework is still lacking, despite the fact that bivalve mitochondrial genomes are unusual under different aspects. In this work, we constructed a dataset of one hundred mitochondrial genomes of bivalves to perform the first systematic comparative mitogenomic analysis, developing a phylogenetic background to scaffold the evolutionary history of the class' mitochondrial genomes. Highly conserved domains were identified in all protein coding genes; however, four genes (namely, atp6, nad2, nad4L, and nad6) were found to be very divergent for many respects, notwithstanding the overall purifying selection working on those genomes. Moreover, the atp8 gene was newly annotated in 20 mitochondrial genomes, where it was previously declared as lacking or only signaled. Supernumerary mitochondrial proteins were compared, but it was possible to find homologies only among strictly related species. The rearrangement rate on the molecule is too high to be used as a phylogenetic marker, but here we demonstrate for the first time in mollusks that there is correlation between rearrangement rates and evolutionary rates. We also developed a new index (HERMES) to estimate the amount of mitochondrial evolution. Many genomic features are phylogenetically congruent and this allowed us to highlight three main phases in bivalve history: the origin, the branching of palaeoheterodonts, and the second radiation leading to the present-day biodiversity.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
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