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Gomes-Dos-Santos A, Fonseca E, Riccardi N, Hinzmann M, Lopes-Lima M, Froufe E. The transcriptome assembly of the European freshwater mussel Unio elongatulus C. Pfeiffer, 1825. Sci Data 2024; 11:377. [PMID: 38609426 PMCID: PMC11014934 DOI: 10.1038/s41597-024-03226-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Freshwater mussels of the order Unionida are a global conservation concern. Species of this group are strictly freshwater, sessile, slow-growing animals and, extremely sensitive to environmental changes. Human-mediated changes in freshwater habitats are imposing enormous pressure on the survival of freshwater mussels. Although a few flagship species are protected in Europe, other highly imperilled species receive much less attention. Moreover, knowledge about biology, ecology, and evolution and proper conservation assessments of many European species are still sparse. This knowledge gap is further aggravated by the lack of genomic resources available, which are key tools for conservation. Here we present the transcriptome assembly of Unio elongatulus C. Pfeiffer, 1825, one of the least studied European freshwater mussels. Using the individual sequencing outputs from eight physiologically representative mussel tissues, we provide an annotated panel of tissue-specific Relative Gene Expression profiles. These resources are pivotal to studying the species' biological and ecological features, as well as helping to understand its vulnerability to current and future threats.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.
| | - Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal
| | | | - Mariana Hinzmann
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal
| | - Manuel Lopes-Lima
- BIOPOLIS Program in Genomics, Biodiversity and Ecosystems, CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- IUCN SSC Mollusc Specialist Group, c/o IUCN, Cambridge, UK
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.
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2
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Nicolini F, Ghiselli F, Luchetti A, Milani L. Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View. Genome Biol Evol 2023; 15:evad181. [PMID: 37850870 PMCID: PMC10588774 DOI: 10.1093/gbe/evad181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023] Open
Abstract
Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition between environmental and genetic SD, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); 2) the genomic evolution of sex chromosomes (SCs), considering that no heteromorphic SCs are currently known and that homomorphic SCs have been identified only in a few species of scallops; 3) the putative role of mitochondria at some level of the SD signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; 4) the evolutionary history of SD-related gene (SRG) families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve SD, as our current knowledge is quite fragmented and limited to a few species. As a matter of fact, tracing the phylogenetic history and diversity of SRG families (such as the Dmrt, Sox, and Fox genes) would allow not only to perform more targeted functional experiments and genomic analyses, but also to foster the possibility of establishing a solid comparative framework.
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Affiliation(s)
- Filippo Nicolini
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
- Fano Marine Center, Fano, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
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3
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Gomes-Dos-Santos A, Lopes-Lima M, Machado MA, Teixeira A, C Castro LF, Froufe E. PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793. Sci Data 2023; 10:340. [PMID: 37264040 DOI: 10.1038/s41597-023-02251-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023] Open
Abstract
Mussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species widely dispersed across world freshwater ecosystems. They are highly threatened showing the highest record of extinction events within faunal taxa. Conservation is particularly concerning in species occurring in the Mediterranean biodiversity hotspot that are exposed to multiple anthropogenic threats, possibly acting in synergy. That is the case of the dolphin freshwater mussel Unio delphinus Spengler, 1793, endemic to the western Iberian Peninsula with recently strong population declines. To date, only four genome assemblies are available for the order Unionida and only one European species. We present the first genome assembly of Unio delphinus. We used the PacBio HiFi to generate a highly contiguous genome assembly. The assembly is 2.5 Gb long, possessing 1254 contigs with a contig N50 length of 10 Mbp. This is the most contiguous freshwater mussel genome assembly to date and is an essential resource for investigating the species' biology and evolutionary history that ultimately will help to support conservation strategies.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P, 4450-208, Matosinhos, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal.
| | - Manuel Lopes-Lima
- BIOPOLIS Program in Genomics, Biodiversity and Ecosystems, CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.
- IUCN SSC Mollusc Specialist Group, c/o IUCN, David Attenborough Building, Pembroke St, Cambridge, England.
| | - M André Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - Amílcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P, 4450-208, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P, 4450-208, Matosinhos, Portugal.
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4
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Xu R, Martelossi J, Smits M, Iannello M, Peruzza L, Babbucci M, Milan M, Dunham JP, Breton S, Milani L, Nuzhdin SV, Bargelloni L, Passamonti M, Ghiselli F. Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam. Genome Biol Evol 2022; 14:6889380. [PMID: 36508337 PMCID: PMC9803972 DOI: 10.1093/gbe/evac171] [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] [Received: 09/11/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.
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Affiliation(s)
- Ran Xu
- Corresponding authors: E-mail: (R.X.); E-mail: (F.G.)
| | | | | | | | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Joseph P Dunham
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA,SeqOnce Biosciences Inc., Pasadena, CA, USA
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
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5
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Han W, Liu L, Wang J, Wei H, Li Y, Zhang L, Guo Z, Li Y, Liu T, Zeng Q, Xing Q, Shu Y, Wang T, Yang Y, Zhang M, Li R, Yu J, Pu Z, Lv J, Lian S, Hu J, Hu X, Bao Z, Bao L, Zhang L, Wang S. Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation. Nat Ecol Evol 2022; 6:1891-1906. [PMID: 36280781 DOI: 10.1038/s41559-022-01898-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/05/2022] [Indexed: 12/15/2022]
Abstract
Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies. The long-term undifferentiation of molluscan sex chromosomes is potentially sustained by the unexpected intertwined regulation of reversible sex-biased genes, together with the lack of sexual dimorphism and occasional sex chromosome turnover. The pleiotropic constraint of regulation of reversible sex-biased genes is widely present in ancient homomorphic sex chromosomes and might be resolved in heteromorphic sex chromosomes through gene duplication followed by subfunctionalization. The evolutionary dynamics of sex chromosomes suggest a mechanism for 'inheritance' turnover of sex-determining genes that is mediated by translocation of a sex-determining enhancer. On the basis of these findings, we propose an evolutionary model for the long-term preservation of homomorphic sex chromosomes.
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Affiliation(s)
- Wentao Han
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liangjie Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Huilan Wei
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lijing Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhenyi Guo
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yajuan Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tian Liu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Qiang Xing
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ya Shu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tong Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yaxin Yang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Meiwei Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ruojiao Li
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiachen Yu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jia Lv
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shanshan Lian
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Xiaoli Hu
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China.
| | - Lingling Zhang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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6
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Gomes-Dos-Santos A, Machado AM, Castro LFC, Prié V, Teixeira A, Lopes-Lima M, Froufe E. The gill transcriptome of threatened European freshwater mussels. Sci Data 2022; 9:494. [PMID: 35963883 PMCID: PMC9376081 DOI: 10.1038/s41597-022-01613-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/27/2022] [Indexed: 11/24/2022] Open
Abstract
Genomic tools applied to non-model organisms are critical to design successful conservation strategies of particularly threatened groups. Freshwater mussels of the Unionida order are among the most vulnerable taxa and yet almost no genetic resources are available. Here, we present the gill transcriptomes of five European freshwater mussels with high conservation concern: Margaritifera margaritifera, Unio crassus, Unio pictorum, Unio mancus and Unio delphinus. The final assemblies, with N50 values ranging from 1069–1895 bp and total BUSCO scores above 90% (Eukaryote and Metazoan databases), were structurally and functionally annotated, and made available. The transcriptomes here produced represent a valuable resource for future studies on these species’ biology and ultimately guide their conservation. Measurement(s) | transcriptomics | Technology Type(s) | Illumina sequencing | Sample Characteristic - Organism | Margaritifera margaritifera • Unio crassus • Unio delphinus • Unio mancus • Unio pictorum | Sample Characteristic - Location | Europe |
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal.
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal
| | - Vincent Prié
- National Museum of Natural History (MNHN), CNRS, SU, EPHE, UA CP 51, 57 rue Cuvier, 75005, Paris, France
| | - Amílcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.,CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,IUCN SSC Mollusc Specialist Group, c/o IUCN, David Attenborough Building, Pembroke St., Cambridge, England
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208, Matosinhos, Portugal.
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7
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Evensen KG, Robinson WE, Krick K, Murray HM, Poynton HC. Comparative phylotranscriptomics reveals putative sex differentiating genes across eight diverse bivalve species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100952. [PMID: 34952324 DOI: 10.1016/j.cbd.2021.100952] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Mollusks, especially bivalves, exhibit a great diversity of sex determining mechanisms, including both genetic and environmental sex determination. Some bivalve species can be gonochoristic (separate sexes), while others are hermaphroditic (sequential or simultaneous). Several models have been proposed for specific bivalve species, utilizing information gained from gene expression data, as well as limited RAD-seq data (e.g., from Crassostrea gigas). However, these mechanisms are not as well studied as those in model organisms (e.g., Mus musculus, Drosophila melanogaster, Caenorhabditis elegans) and many genes involved in sex differentiation are not well characterized. We used phylotranscriptomics to better understand which possible sex differentiating genes are in bivalves and how these genes relate to similar genes in diverse phyla. We collected RNAseq data from eight phylogenetically diverse bivalve species: Argopecten irradians, Ensis directus, Geukensia demissa, Macoma tenta, Mercenaria mercenaria, Mya arenaria, Mytilus edulis, and Solemya velum. Using these data, we assembled representative transcriptomes for each species. We then searched for candidate sex differentiating genes using BLAST and confirmed the identity of nine genes using phylogenetics analyses from nine phyla. To increase the confidence of identification, we included ten bivalve genomes in our analyses. From the analysis of doublesex and mab-3 related transcription factor (DMRT) genes, we confirmed the identify of a Mollusk-specific sex determining DMRT gene: DMRT1L. Based on gene expression data from M. edulis and previous research, DMRT1L and FoxL2 are key genes for male and female development, respectively.
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Affiliation(s)
- K Garrett Evensen
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - William E Robinson
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - Keegan Krick
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - Harry M Murray
- Department of Fisheries and Oceans Canada, 80 East White Hills Road, St John's, NL A1C 5X1, Canada
| | - Helen C Poynton
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America.
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8
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Breton S, Stewart DT, Brémaud J, Havird JC, Smith CH, Hoeh WR. Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system? Bioessays 2022; 44:e2100283. [PMID: 35170770 PMCID: PMC9083018 DOI: 10.1002/bies.202100283] [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: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 01/10/2023]
Abstract
Animal and plant species exhibit an astonishing diversity of sexual systems, including environmental and genetic determinants of sex, with the latter including genetic material in the mitochondrial genome. In several hermaphroditic plants for example, sex is determined by an interaction between mitochondrial cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Specifically, CMS involves aberrant mitochondrial genes that prevent pollen development and specific nuclear genes that restore it, leading to a mixture of female (male-sterile) and hermaphroditic individuals in the population (gynodioecy). Such a mitochondrial-nuclear sex determination system is thought to be rare outside plants. Here, we present one possible case of CMS in animals. We hypothesize that the only exception to the strict maternal mtDNA inheritance in animals, the doubly uniparental inheritance (DUI) system in bivalves, might have originated as a mitochondrial-nuclear sex-determination system. We document and explore similarities that exist between DUI and CMS, and we propose various ways to test our hypothesis.
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Affiliation(s)
- Sophie Breton
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Julie Brémaud
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chase H Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Walter R Hoeh
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
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9
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Lattos A, Feidantsis K, Georgoulis I, Giantsis IA, Karagiannis D, Theodorou JA, Staikou A, Michaelidis B. Pathophysiological Responses of Pinna nobilis Individuals Enlightens the Etiology of Mass Mortality Situation in the Mediterranean Populations. Cells 2021; 10:2838. [PMID: 34831063 PMCID: PMC8616554 DOI: 10.3390/cells10112838] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 12/31/2022] Open
Abstract
Due to the rapid decrease of Pinna nobilis populations during the previous decades, this bivalve species, endemic in the Mediterranean Sea, is characterized as 'critically endangered'. In addition to human pressures, various pathogen infections have resulted in extended reduction, even population extinction. While Haplosporidium pinnae is characterized as one of the major causative agents, mass mortalities have also been attributed to Mycobacterium sp. and Vibrio spp. Due to limited knowledge concerning the physiological response of infected P. nobilis specimens against various pathogens, this study's aim was to investigate to pathophysiological response of P. nobilis individuals, originating from mortality events in the Thermaikos Gulf and Lesvos and Limnos islands (Greece), and their correlation to different potential pathogens detected in the diseased animals. In isolated tissues, several cellular stress indicators of the heat shock and immune response, apoptosis and autophagy, were examined. Despite the complexity and limitations in the study of P. nobilis mortality events, the present investigation demonstrates the cumulative negative effect of co-infection additionally with H. pinnae in comparison to the non-presence of haplosporidian parasite. In addition, impacts of global climate change affecting physiological performance and immune responses result in more vulnerable populations in infectious diseases, a phenomenon which may intensify in the future.
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Affiliation(s)
- Athanasios Lattos
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.L.); (K.F.); (I.G.)
| | - Konstantinos Feidantsis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.L.); (K.F.); (I.G.)
| | - Ioannis Georgoulis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.L.); (K.F.); (I.G.)
| | - Ioannis A. Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece;
| | - Dimitrios Karagiannis
- National Reference Laboratory for Mollusc Diseases, Ministry of Rural Development and Food, 54627 Thessaloniki, Greece;
| | - John A. Theodorou
- Department of Animal Production Fisheries & Aquaculture, University of Patras, 26504 Mesolonghi, Greece;
| | - Alexandra Staikou
- Laboratory of Zoology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.L.); (K.F.); (I.G.)
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10
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Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
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11
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de Melo KP, Camargo M. Mechanisms for sperm mitochondrial removal in embryos. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118916. [PMID: 33276010 DOI: 10.1016/j.bbamcr.2020.118916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Different animal species have different characteristics regarding the transmission of mitochondrial DNA. While some species have biparental mitochondrial inheritance, others have developed pathways to remove paternal mtDNA. These pathways guarantee the uniparental mitochondrial inheritance, so far well known in mammals, avoiding heteroplasmy, which may have the potential to cause certain mitochondrial diseases in the offspring. SCOPE OF REVIEW This review aims to address the main mechanisms that involve mitochondrial degradation in different animal species, as well as to describe what is present in the literature on the mechanisms involved in mitochondrial inheritance. MAJOR CONCLUSIONS Two theories are proposed to explain the uniparental inheritance of mtDNA: (i) active degradation, where mechanisms for paternal mitochondrial DNA elimination involve mitochondrial degradation pathway by autophagy and, in some species, may also involve the endocytic degradation pathway; and (ii) passive dilution, where the paternal mitochondria are diluted in the cells of the embryo according to cell division, until becoming undetectable. GENERAL SIGNIFICANCE This work brings a wide review of the already published evidence on mitochondrial inheritance in the animal kingdom and the possible mechanisms to mtDNA transmission already described in literature.
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Affiliation(s)
- Karla Pacheco de Melo
- Department of Surgery, Division of Urology, Human Reproduction Section, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Camargo
- Department of Surgery, Division of Urology, Human Reproduction Section, Universidade Federal de São Paulo, São Paulo, Brazil.
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12
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Passamonti M, Plazzi F. Doubly Uniparental Inheritance and beyond: The contribution of the Manila clamRuditapes philippinarum. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marco Passamonti
- Department of Biological, Geological, and Environmental Sciences University of Bologna Bologna Italy
| | - Federico Plazzi
- Department of Biological, Geological, and Environmental Sciences University of Bologna Bologna Italy
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13
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Milani L, Ghiselli F. Faraway, so close. The comparative method and the potential of non-model animals in mitochondrial research. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190186. [PMID: 31787048 DOI: 10.1098/rstb.2019.0186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inference from model organisms has been the engine for many discoveries in life science, but indiscriminate generalization leads to oversimplifications and misconceptions. Model organisms and inductive reasoning are irreplaceable: there is no other way to tackle the complexity of living systems. At the same time, it is not advisable to infer general patterns from a restricted number of species, which are very far from being representative of the diversity of life. Not all models are equal. Some organisms are suitable to find similarities across species, other highly specialized organisms can be used to focus on differences. In this opinion piece, we discuss the dominance of the mechanistic/reductionist approach in life sciences and make a case for an enhanced application of the comparative approach to study processes in all their various forms across different organisms. We also enlist some rising animal models in mitochondrial research, to exemplify how non-model organisms can be chosen in a comparative framework. These taxa often do not possess implemented tools and dedicated methods/resources. However, because of specific features, they have the potential to address still unanswered biological questions. Finally, we discuss future perspectives and caveats of the comparative method in the age of 'big data'. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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14
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Capt C, Renaut S, Stewart DT, Johnson NA, Breton S. Putative Mitochondrial Sex Determination in the Bivalvia: Insights From a Hybrid Transcriptome Assembly in Freshwater Mussels. Front Genet 2019; 10:840. [PMID: 31572447 PMCID: PMC6754070 DOI: 10.3389/fgene.2019.00840] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/13/2019] [Indexed: 11/13/2022] Open
Abstract
Bivalves exhibit an astonishing diversity of sexual systems, with genetic and environmental determinants of sex, and possibly the only example of mitochondrial genes influencing sex determination pathways in animals. In contrast to all other animal species in which strict maternal inheritance (SMI) of mitochondria is the rule, bivalves possess a system known as doubly uniparental inheritance (DUI) of mitochondria in which maternal and paternal mitochondria (and their corresponding female-transmitted or F mtDNA and male-transmitted or M mtDNA genomes) are transmitted within a species. Species with DUI also possess sex-associated mtDNA-encoded proteins (in addition to the typical set of 13), which have been hypothesized to play a role in sex determination. In this study, we analyzed the sex-biased transcriptome in gonads of two closely-related freshwater mussel species with different reproductive and mitochondrial transmission modes: the gonochoric, DUI species, Utterbackia peninsularis, and the hermaphroditic, SMI species, Utterbackia imbecillis. Through comparative analysis with other DUI and non-DUI bivalve transcriptomes already available, we identify common male and female-specific genes, as well as SMI and DUI-related genes, that are probably involved in sex determination and mitochondrial inheritance in this animal group. Our results contribute to the understanding of what could be the first animal sex determination system involving the mitochondrial genome.
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Affiliation(s)
- Charlotte Capt
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada
| | - Sébastien Renaut
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada.,Centre de la Science de la Biodiversité du Québec, Université de Montréal, Montréal, QC, Canada
| | | | - Nathan A Johnson
- Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL, United States
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada
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15
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Chacón GM, Arias‐Pérez A, Freire R, Martínez L, Nóvoa S, Naveira H, Insua A. Evidence of doubly uniparental inheritance of the mitochondrial
DNA
in
Polititapes rhomboides
(Bivalvia, Veneridae): Evolutionary and population genetic analysis of F and M mitotypes. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ginna M. Chacón
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Alberto Arias‐Pérez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ruth Freire
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Luisa Martínez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Susana Nóvoa
- Centro de Cultivos Marinos de Ribadeo‐CIMAXunta de Galicia Ribadeo (Lugo) Spain
| | - Horacio Naveira
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ana Insua
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
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16
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Angers A, Ouimet P, Tsyvian-Dzyabko A, Nock T, Breton S. [The underestimated coding potential of mitochondrial DNA]. Med Sci (Paris) 2019; 35:46-54. [PMID: 30672456 DOI: 10.1051/medsci/2018308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mitochondria are ancient organelles that emerged from the endosymbiosis of free-living proto-bacteria. They still retain a semi-autonomous genetic system with a small genome. Mitochondrial DNA (mtDNA) codes for 13 essential proteins for the production of ATP, the sequences of which are relatively conserved across Metazoans. The discovery of additional mitochondria-derived peptides (MDPs) indicates an underestimated coding potential. Humanin, an anti-apoptotic peptide, is likely independently transcribed from within the 16S rRNA gene, as are recently described SHLPs. MOTS-c, discovered in silico, has been demonstrated to be involved in metabolism and insulin sensitivity. Gau, is a positionally conserved open reading frame (ORF) sequence found in the antisense strand of the COX1 gene and its corresponding peptide is strictly colocalized with mitochondrial markers. In bivalves with doubly uniparental inheritance of mtDNA, male and female mtDNAs each carry a separate additional gene possibly involved in sex determination. Other MDPs likely exist and their investigation will shed light on the underestimated functional repertoire of mitochondria.
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Affiliation(s)
- Annie Angers
- Département de sciences biologiques, université de Montréal, pavillon Marie-Victorin, faculté des arts et des sciences. CP 6128, succursale centre-ville, Montréal QC, H3C 3J7, Canada
| | - Philip Ouimet
- Département de sciences biologiques, université de Montréal, pavillon Marie-Victorin, faculté des arts et des sciences. CP 6128, succursale centre-ville, Montréal QC, H3C 3J7, Canada
| | - Assia Tsyvian-Dzyabko
- Département de sciences biologiques, université de Montréal, pavillon Marie-Victorin, faculté des arts et des sciences. CP 6128, succursale centre-ville, Montréal QC, H3C 3J7, Canada
| | - Tanya Nock
- Département de sciences biologiques, université de Montréal, pavillon Marie-Victorin, faculté des arts et des sciences. CP 6128, succursale centre-ville, Montréal QC, H3C 3J7, Canada
| | - Sophie Breton
- Département de sciences biologiques, université de Montréal, pavillon Marie-Victorin, faculté des arts et des sciences. CP 6128, succursale centre-ville, Montréal QC, H3C 3J7, Canada
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17
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Renaut S, Guerra D, Hoeh WR, Stewart DT, Bogan AE, Ghiselli F, Milani L, Passamonti M, Breton S. Genome Survey of the Freshwater Mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) Using a Hybrid De Novo Assembly Approach. Genome Biol Evol 2018; 10:1637-1646. [PMID: 29878181 PMCID: PMC6054159 DOI: 10.1093/gbe/evy117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2018] [Indexed: 02/03/2023] Open
Abstract
Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission of freshwater mussels. The genome described here was obtained by combining high-coverage short reads (65× genome coverage of Illumina paired-end and 11× genome coverage of mate-pairs sequences) with low-coverage Pacific Biosciences long reads (0.3× genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54 Gb (366,926 scaffolds, N50 = 6.5 kb, with 2.3% of “N” nucleotides), representing 86% of the predicted genome size of 1.80 Gb, while over one third of the genome (37.5%) consisted of repeated elements and >85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.
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Affiliation(s)
- Sébastien Renaut
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Canada.,Quebec Centre for Biodiversity Science, Montréal, Québec, Canada
| | - Davide Guerra
- Département de Sciences Biologiques, Université de Montréal, Canada
| | - Walter R Hoeh
- Department of Biological Sciences, Kent State University
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina
| | - Fabrizio Ghiselli
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Italy
| | - Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Italy
| | - Marco Passamonti
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, University of Bologna, Italy
| | - Sophie Breton
- Quebec Centre for Biodiversity Science, Montréal, Québec, Canada.,Département de Sciences Biologiques, Université de Montréal, Canada
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18
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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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