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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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Patnaik HH, Sang MK, Park JE, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Patnaik BB, Lee YS. A review of the endangered mollusks transcriptome under the threatened species initiative of Korea. Genes Genomics 2023:10.1007/s13258-023-01389-3. [PMID: 37405596 DOI: 10.1007/s13258-023-01389-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/09/2023] [Indexed: 07/06/2023]
Abstract
Transcriptome studies for conservation of endangered mollusks is a proactive approach towards managing threats and uncertainties facing these species in natural environments. The population of these species is declining due to habitat destruction, illicit wildlife trade, and global climate change. These activities risk the free movement of species across the wild landscape, loss of breeding grounds, and restrictions in displaying the physiological attributes so crucial for faunal welfare. Gastropods face the most negative ecological effects and have been enlisted under Korea's protective species consortium based on their population dynamics in the last few years. Moreover, with the genetic resources restricted for such species, conservation by informed planning is not possible. This review provides insights into the activities under the threatened species initiative of Korea with special reference to the transcriptome assemblies of endangered mollusks. The gastropods such as Ellobium chinense, Aegista chejuensis, Aegista quelpartensis, Incilaria fruhstorferi, Koreanohadra kurodana, Satsuma myomphala, and Clithon retropictus have been represented. Moreover, the transcriptome summary of bivalve Cristaria plicata and Caenogastropoda Charonia lampas sauliae is also discussed. Sequencing, de novo assembly, and annotation identified transcripts or homologs for the species and, based on an understanding of the biochemical and molecular pathways, were ascribed to predictive gene function. Mining for simple sequence repeats from the transcriptome have successfully assisted genetic polymorphism studies. A comparison of the transcriptome scheme of Korean endangered mollusks with the genomic resources of other endangered mollusks have been discussed with homologies and analogies for dictating future research.
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Affiliation(s)
- Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, 37242, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, 56212, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, Chungnam, 31539, South Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- P.G Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, 756089, Nuapadhi, Balasore, India
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea.
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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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Mejia-Trujillo R, Smith CH. The male-type mitochondrial genome of the freshwater mussel Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019 (Bivalvia: Unionidae). Mitochondrial DNA B Resour 2022; 7:1854-1858. [PMID: 36325280 PMCID: PMC9621207 DOI: 10.1080/23802359.2022.2134750] [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] [Indexed: 11/06/2022] Open
Abstract
The global decline of freshwater mussels emphasizes the need to establish genetic resources to better understand their biology, including a unique mitochondrial biology known as doubly uniparental inheritance. In this study, we present the complete male-type (M-type) mitochondrial genome of the freshwater mussel, Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019. The M-type mtDNA is approximately 16 kilobases and contains 22 tRNAs, two rRNAs, and 14 protein-coding genes, including a male-specific open reading frame. Read coverage revealed that M-type mtDNA was more abundant than female-type mtDNA in male gonadal tissue, with respect to a non-spawning male individual. Novel mitogenomes were resolved within previously described sex-specific monophyletic clades across the subfamily Ambleminae. The availability of high-quality nuclear and mitochondrial genomic data for P. streckersoni makes it a model for future research into the potential role of mtDNA in sex determination or sexual development in freshwater mussels.
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Affiliation(s)
| | - Chase H. Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA,CONTACT Chase H. Smith Department of Integrative Biology, University of Texas, Austin, TX, USA
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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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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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8
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Bettinazzi S, Milani L, Blier PU, Breton S. Bioenergetic consequences of sex-specific mitochondrial DNA evolution. Proc Biol Sci 2021; 288:20211585. [PMID: 34403637 PMCID: PMC8370797 DOI: 10.1098/rspb.2021.1585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Abstract
Doubly uniparental inheritance (DUI) represents a notable exception to the general rule of strict maternal inheritance (SMI) of mitochondria in metazoans. This system entails the coexistence of two mitochondrial lineages (F- and M-type) transmitted separately through oocytes and sperm, thence providing an unprecedented opportunity for the mitochondrial genome to evolve adaptively for male functions. In this study, we explored the impact of a sex-specific mitochondrial evolution upon gamete bioenergetics of DUI and SMI bivalve species, comparing the activity of key enzymes of glycolysis, fermentation, fatty acid metabolism, tricarboxylic acid cycle, oxidative phosphorylation and antioxidant metabolism. Our findings suggest reorganized bioenergetic pathways in DUI gametes compared to SMI gametes. This generally results in a decreased enzymatic capacity in DUI sperm with respect to DUI oocytes, a limitation especially prominent at the terminus of the electron transport system. This bioenergetic remodelling fits a reproductive strategy that does not require high energy input and could potentially link with the preservation of the paternally transmitted mitochondrial genome in DUI species. Whether this phenotype may derive from positive or relaxed selection acting on DUI sperm is still uncertain.
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Affiliation(s)
- Stefano Bettinazzi
- Département de sciences biologiques, Université de Montréal, Montréal, Quebec, Canada H2V 2S9
| | - Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna 40126, Italia
| | - Pierre U. Blier
- Département de biologie, Université du Québec à Rimouski, Rimouski, Quebec, Canada G5 L 3A1
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, Montréal, Quebec, Canada H2V 2S9
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9
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Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021; 13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
- Biology Department, Baylor University, Waco, Texas, USA
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10
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Wang YY, Duan SH, Wang GL, Li JL. Integrated mRNA and miRNA expression profile analysis of female and male gonads in Hyriopsis cumingii. Sci Rep 2021; 11:665. [PMID: 33436779 PMCID: PMC7804246 DOI: 10.1038/s41598-020-80264-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Hyriopsis cumingii is an important species for freshwater pearl cultivation in China. In terms of pearl production, males have larger pearls and better glossiness than females, but there are few reports focusing on the sex of H. cumingii. In this study, six mRNA and six microRNA (miRNA) libraries were prepared from ovaries and testes. Additionally, 28,502 differentially expressed genes (DEGs) and 32 differentially expressed miRNAs (DEMs) were identified. Compared with testis, 14,360 mRNAs and 20 miRNAs were up-regulated in ovary, 14,142 mRNAs and 12 miRNAs were down-regulated. In DEGs, the known genes related to sex determinism and/or differentiation were also identified, such as DMRT1, SOX9, SF1 for males, FOXL2 for females, and other potentially significant candidate genes. Three sex-related pathways have also been identified, which are Wnt, Notch, and TGF-beta. In 32 DEMs, the three miRNAs (miR-9-5p, miR-92, miR-184) were paid more attention, they predicted 28 target genes, which may also be candidates for sex-related miRNAs and genes. Differential miRNAs target genes analysis reveals the pathway associated with oocyte meiosis and spermatogenesis. Overall, the findings of the study provide significant insights to enhance our understanding of sex differentiation and/or sex determination mechanisms for H. cumingii.
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Affiliation(s)
- Ya-Yu Wang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Sheng-Hua Duan
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Gui-Ling Wang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
| | - Jia-Le Li
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai, 201306 China ,National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306 China ,Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306 China
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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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Lubośny M, Przyłucka A, Śmietanka B, Burzyński A. Semimytilus algosus: first known hermaphroditic mussel with doubly uniparental inheritance of mitochondrial DNA. Sci Rep 2020; 10:11256. [PMID: 32647112 PMCID: PMC7347871 DOI: 10.1038/s41598-020-67976-6] [Citation(s) in RCA: 9] [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: 03/23/2020] [Accepted: 06/11/2020] [Indexed: 11/08/2022] Open
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA is a rare phenomenon occurring in some freshwater and marine bivalves and is usually characterized by the mitochondrial heteroplasmy of male individuals. Previous research on freshwater Unionida mussels showed that hermaphroditic species do not have DUI even if their closest gonochoristic counterparts do. No records showing DUI in a hermaphrodite have ever been reported. Here we show for the first time that the hermaphroditic mussel Semimytilus algosus (Mytilida), very likely has DUI, based on the complete sequences of both mitochondrial DNAs and the distribution of mtDNA types between male and female gonads. The two mitogenomes show considerable divergence (34.7%). The presumably paternal M type mitogenome dominated the male gonads of most studied mussels, while remaining at very low or undetectable levels in the female gonads of the same individuals. If indeed DUI can function in the context of simultaneous hermaphroditism, a change of paradigm regarding its involvement in sex determination is needed. It is apparently associated with gonadal differentiation rather than with sex determination in bivalves.
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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
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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Soroka M. Doubly uniparental inheritance of mitochondrial DNA in freshwater mussels: History and status of the European species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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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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