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Luo L, Wang M, Liu Y, Li J, Bu F, Yuan H, Tang R, Liu C, He G. Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm. SCIENCE CHINA. LIFE SCIENCES 2025; 68:1610-1625. [PMID: 39843848 DOI: 10.1007/s11427-024-2736-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/18/2024] [Indexed: 01/24/2025]
Abstract
Human mitochondrial DNA (mtDNA) harbors essential mutations linked to aging, neurodegenerative diseases, and complex muscle disorders. Due to its uniparental and haploid inheritance, mtDNA captures matrilineal evolutionary trajectories, playing a crucial role in population and medical genetics. However, critical questions about the genomic diversity patterns, inheritance models, and evolutionary and medical functions of mtDNA remain unresolved or underexplored, particularly in the transition from traditional genotyping to large-scale genomic analyses. This review summarizes recent advancements in data-driven genomic research and technological innovations that address these questions and clarify the biological impact of nuclear-mitochondrial segments (NUMTs) and mtDNA variants on human health, disease, and evolution. We propose a streamlined pipeline to comprehensively identify mtDNA and NUMT genomic diversity using advanced sequencing and computational technologies. Haplotype-resolved mtDNA sequencing and assembly can distinguish authentic mtDNA variants from NUMTs, reduce diagnostic inaccuracies, and provide clearer insights into heteroplasmy patterns and the authenticity of paternal inheritance. This review emphasizes the need for integrative multi-omics approaches and emerging long-read sequencing technologies to gain new insights into mutation mechanisms, the influence of heteroplasmy and paternal inheritance on mtDNA diversity and disease susceptibility, and the detailed functions of NUMTs.
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Affiliation(s)
- Lintao Luo
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
| | - Yunhui Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Jianbo Li
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
| | - Chao Liu
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
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2
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Leroux É, Khorami HH, Angers A, Angers B, Breton S. Mitochondrial epigenetics brings new perspectives on doubly uniparental inheritance in bivalves. Sci Rep 2024; 14:31544. [PMID: 39733193 PMCID: PMC11682101 DOI: 10.1038/s41598-024-83368-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 12/13/2024] [Indexed: 12/30/2024] Open
Abstract
Mitochondrial epigenetics, particularly mtDNA methylation, is a flourishing field of research. MtDNA methylation appears to play multiple roles, including regulating mitochondrial transcription, cell metabolism and mitochondrial inheritance. In animals, bivalves with doubly uniparental inheritance (DUI) of mitochondria are the exception to the rule of maternal mitochondrial inheritance since DUI also involve a paternal mtDNA transmitted from the father to sons. The mechanisms underlying DUI are still unknown, but mtDNA methylation could play a role in its regulation. Here, we investigated mtDNA methylation levels and machinery in gonads of the mussel Mytilus edulis using methods based on antibodies, enzymatic cleavage and methylome sequencing. Our results confirm the presence in mitochondria of methylated cytosines and adenines and methyltransferases and unveil a more variable cytosine methylation state among males than females. Also, spermatid mtDNA is always methylated, while only few spermatozoa present methylated mtDNA suggesting a relation between cytosine methylation and development stage of male gametes. We propose that mtDNA methylation could play a role in the different fates of the parental mtDNAs in male and female embryos in M. edulis. Our study provides novel insights into the epigenetic landscape of bivalve mtDNA and highlights the multiple roles of mtDNA methylation in animals.
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Affiliation(s)
- Émélie Leroux
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada.
| | | | - Annie Angers
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada
| | - Bernard Angers
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal, Montréal, QC, Canada.
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3
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Liu X, Liu N, Jing X, Khan H, Yang K, Zheng Y, Nie Y, Song H, Huang Y. Genomic and transcriptomic perspectives on the origin and evolution of NUMTs in Orthoptera. Mol Phylogenet Evol 2024; 201:108221. [PMID: 39454737 DOI: 10.1016/j.ympev.2024.108221] [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: 03/21/2024] [Revised: 10/08/2024] [Accepted: 10/21/2024] [Indexed: 10/28/2024]
Abstract
Nuclear mitochondrial pseudogenes (NUMTs) result from the transfer of mitochondrial DNA (mtDNA) to the nuclear genome. NUMTs, as "frozen" snapshots of mitochondria, can provide insights into diversification patterns. In this study, we analyzed the origins and insertion frequency of NUMTs using genome assembly data from ten species in Orthoptera. We found divergences between NUMTs and contemporary mtDNA in Orthoptera ranging from 0 % to 23.78 %. The results showed that the number of NUMT insertions was significantly positively correlated with the content of transposable elements in the genome. We found that 39.09 %-68.65 % of the NUMTs flanking regions (2,000 bp) contained retrotransposons, and more NUMTs originated from mitochondrial rDNA regions. Based on the analysis of the mitochondrial transcriptome, we found a potential mechanism of NUMT integration: mitochondrial transcripts are reverse transcribed into double-stranded DNA and then integrated into the genome. The probability of this mechanism occurring accounts for 0.30 %-1.02 % of total mitochondrial nuclear transfer events. Finally, based on the phylogenetic tree constructed using NUMTs and contemporary mtDNA, we provide insights into ancient evolutionary events such as species-specific "autaponumts" and "synaponumts" shared among different species, as well as post-integration duplication events.
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Affiliation(s)
- Xuanzeng Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Nian Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xuan Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hashim Khan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Kaiyan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yanna Zheng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yimeng Nie
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, USA.
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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4
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Xu T, He C, Han X, Kong L, Li Q. Comparative mitogenomic analysis and phylogeny of Veneridae with doubly uniparental inheritance. Open Biol 2024; 14:240186. [PMID: 39591991 PMCID: PMC11597414 DOI: 10.1098/rsob.240186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 10/21/2024] [Accepted: 10/24/2024] [Indexed: 11/28/2024] Open
Abstract
Doubly uniparental inheritance (DUI) is an atypical animal mtDNA inheritance system, reported so far only in bivalve species, in which two mitochondrial lineages exist: one transmitted through the egg (F-type) and the other through the sperm (M-type). Although numerous species exhibit this unusual organelle inheritance, it is primarily documented in marine and freshwater mussels. The distribution, function and molecular evolutionary implications of DUI in the family Veneridae, however, remain unclear. Here, we investigated 17 species of Veneridae, compared mitochondrial genomes of DUI species and reconstructed their phylogenetic framework. Different sex-linked mitochondrial genomes have been identified in the male gonads and adductor muscles of 7 venerids, indicating the presence of DUI in these species. Analysis of the unassigned regions (URs) of the mitochondrial genome in DUI species revealed that 13 out of 44 URs contained repetitive sequences, with nine being long unassigned regions (LURs). All LURs were capable of forming secondary structures, and most of them exhibited patterns of significant sequence similarity to elements known to have specific functions in the control regions of sea urchins and mammals. The F/M phylogeny showed that DUI venerids exhibit both taxon-specific patterns and gender-specific patterns, with Gafrarium dispar experiencing masculinization events.
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Affiliation(s)
- Tao Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, People’s Republic of China
| | - Chuandong He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, People’s Republic of China
| | - Xiao Han
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, People’s Republic of China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, People’s Republic of China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong266237, People’s Republic of China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, People’s Republic of China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong266237, People’s Republic of China
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Smith CH, Mejia-Trujillo R, Havird JC. Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance. Evolution 2024; 78:1790-1803. [PMID: 38995057 PMCID: PMC11519007 DOI: 10.1093/evolut/qpae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/03/2024] [Accepted: 07/11/2024] [Indexed: 07/13/2024]
Abstract
Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males transmit a different mtDNA (M mtDNA) solely to their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded in M mtDNA evolve under relaxed selection due to their function being limited to sperm only (vs. all other tissues for F mtDNA). This has led to the hypothesis that mitonuclear coevolution is less important for M mtDNA. Here, we use comparative phylogenetics, transcriptomics, and proteomics to understand mitonuclear interactions in DUI bivalves. We found nuclear OXPHOS proteins coevolve and maintain compatibility similarly with both F and M mtDNA OXPHOS proteins. Mitochondrial recombination did not influence mitonuclear compatibility and nuclear-encoded OXPHOS genes were not upregulated in tissues with M mtDNA to offset dysfunction. Our results support that selection maintains mitonuclear compatibility with F and M mtDNA despite relaxed selection on M mtDNA. Strict sperm transmission, lower effective population size, and higher mutation rates may explain the evolution of M mtDNA. Our study highlights that mitonuclear coevolution and compatibility may be broad features of eukaryotes.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Raquel Mejia-Trujillo
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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6
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Qi Z, Shi J, Yu Y, Yin G, Zhou X, Yu Y. Paternal Mitochondrial DNA Leakage in Natural Populations of Large-Scale Loach, Paramisgurnus dabryanus. BIOLOGY 2024; 13:604. [PMID: 39194542 DOI: 10.3390/biology13080604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/02/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024]
Abstract
Animal mitochondrial DNA is usually considered to comply with strict maternal inheritance, and only one mitochondrial DNA haplotype exists in an individual. However, mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype, has recently been reported in some animals, such as mice, mussels, and birds. This study conducted extensive field surveys to obtain representative samples to investigate the existence of paternal inheritance of mitochondrial DNA (mtDNA) in natural fish populations. Evidence of paternal mitochondrial DNA leakage of P. dabryanus was discovered using high-throughput sequencing and bioinformatics methods. Two distinct mitochondrial haplotypes (16,569 bp for haplotype I and 16,646 bp for haplotype II) were observed, differing by 18.83% in nucleotide sequence. Phylogenetic analysis suggests divergence between these haplotypes and potential interspecific hybridization with M. anguillicaudatus, leading to paternal leakage. In natural populations of P. dabryanus along the Yangtze River, both haplotypes are present, with Type I being dominant (75% copy number). Expression analysis shows that Type I has higher expression levels of ND3 and ND6 genes compared to Type II, suggesting Type I's primary role. This discovery of a species with two mitochondrial types provides a model for studying paternal leakage heterogeneity and insights into mitochondrial genome evolution and inheritance.
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Affiliation(s)
- Zixin Qi
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaoxu Shi
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Agronomy and Life Science Department, Zhaotong University, Zhaotong 657000, China
| | - Yue Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangmei Yin
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyun Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyao Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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7
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Burzyński A, Śmietanka B, Fernández-Pérez J, Lubośny M. The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species. Sci Rep 2024; 14:14465. [PMID: 38914611 PMCID: PMC11196677 DOI: 10.1038/s41598-024-63764-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 05/31/2024] [Indexed: 06/26/2024] Open
Abstract
Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
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Affiliation(s)
- Artur Burzyński
- 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
| | - Jenyfer Fernández-Pérez
- Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
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8
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Al-Yazeedi T, Adams S, Tandonnet S, Turner A, Kim J, Lee J, Pires-daSilva A. The contribution of an X chromosome QTL to non-Mendelian inheritance and unequal chromosomal segregation in Auanema freiburgense. Genetics 2024; 227:iyae032. [PMID: 38431281 PMCID: PMC11075566 DOI: 10.1093/genetics/iyae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Auanema freiburgense is a nematode with males, females, and selfing hermaphrodites. When XO males mate with XX females, they typically produce a low proportion of XO offspring because they eliminate nullo-X spermatids. This process ensures that most sperm carry an X chromosome, increasing the likelihood of X chromosome transmission compared to random segregation. This occurs because of an unequal distribution of essential cellular organelles during sperm formation, likely dependent on the X chromosome. Some sperm components are selectively segregated into the X chromosome's daughter cell, while others are discarded with the nullo-X daughter cell. Intriguingly, the interbreeding of 2 A. freiburgense strains results in hybrid males capable of producing viable nullo-X sperm. Consequently, when these hybrid males mate with females, they yield a high percentage of male offspring. To uncover the genetic basis of nullo-spermatid elimination and X chromosome drive, we generated a genome assembly for A. freiburgense and genotyped the intercrossed lines. This analysis identified a quantitative trait locus spanning several X chromosome genes linked to the non-Mendelian inheritance patterns observed in A. freiburgense. This finding provides valuable clues to the underlying factors involved in asymmetric organelle partitioning during male meiotic division and thus non-Mendelian transmission of the X chromosome and sex ratios.
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Affiliation(s)
- Talal Al-Yazeedi
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sally Adams
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sophie Tandonnet
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Anisa Turner
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Jun Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear Sex Determination? Empirical Evidence from Bivalves. Mol Biol Evol 2023; 40:msad240. [PMID: 37935058 PMCID: PMC10653589 DOI: 10.1093/molbev/msad240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear sex determination? Empirical evidence from bivalves. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547839. [PMID: 37461691 PMCID: PMC10349986 DOI: 10.1101/2023.07.05.547839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In bivalves, however, mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination in lineages that possess doubly uniparental inheritance (DUI). In these cases, females transmit a female mtDNA (F mtDNA) to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short non-coding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA shed a sncRNA partially within a male-specific mitochondrial gene that targeted pathways hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, non-respiratory functions and provide a first glimpse into an unorthodox sex determining system.
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Affiliation(s)
- Chase H. Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C. Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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11
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Smith CH, Pinto BJ, Kirkpatrick M, Hillis DM, Pfeiffer JM, Havird JC. A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance. J Hered 2023; 114:199-206. [PMID: 36897956 PMCID: PMC10212130 DOI: 10.1093/jhered/esad004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/19/2023] [Indexed: 03/12/2023] Open
Abstract
In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluskan class Bivalvia. The phylogenetic distribution of male-transmitted mitochondrial DNA (M mtDNA) in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female-transmitted mitochondrial DNA (F mtDNA). In this study, we use phylogenetic methods to test M mtDNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of M mtDNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of F mtDNA and M mtDNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination could be connected to the role of M mtDNA in sex determination or sexual development. Our results support that recombination events may occur throughout the mitochondrial genomes of DUI species. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of M mtDNA in protein-coding genes.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Brendan J Pinto
- Center for Evolutionary Medicine & Public Health, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - David M Hillis
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - John M Pfeiffer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX, United States
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12
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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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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: 13] [Impact Index Per Article: 4.3] [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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Matoo OB, Neiman M. Bringing Disciplines and People Together to Characterize the Plastic and Genetic Responses of Molluscs to Environmental Change. Integr Comp Biol 2021; 61:1689-1698. [PMID: 34435639 PMCID: PMC8699093 DOI: 10.1093/icb/icab186] [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] [Indexed: 11/12/2022] Open
Abstract
Molluscs are remarkably diverse and are found across nearly all ecosystems, meaning that members of this ancient animal phylum provide a powerful means to study genomic-phenotype connections in a climate change framework. Recent advances in genomic sequencing technologies and genome assembly approaches finally allow the relatively cheap and tractable assembly of high-quality mollusc genome resources. After a brief review of these issues and advances, we use a case-study approach to provide some concrete examples of phenotypic plasticity and genomic adaptation in molluscs in response to environmental factors expected to be influenced by climate change. Our goal is to use molluscs as a "common currency" to demonstrate how organismal and evolutionary biologists can use natural systems to make phenotype-genotype connections in the context of changing environments. In parallel, we emphasize the critical need to collaborate and integrate findings across taxa and disciplines in order to use new data and information to advance our understanding of mollusc biology in the context of global environmental change. We end with a brief synthetic summary of the papers inspired by the 2021 SICB Symposium "Genomic Perspectives in Comparative Physiology of Molluscs: Integration across Disciplines".
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Affiliation(s)
- Omera B Matoo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln 68588, NE, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City 52242, IA, USA.,Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City 52242, IA, USA
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Distant hybrids of Heliocidaris crassispina (♀) and Strongylocentrotus intermedius (♂): identification and mtDNA heteroplasmy analysis. BMC Evol Biol 2020; 20:101. [PMID: 32781979 PMCID: PMC7422570 DOI: 10.1186/s12862-020-01667-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 11/27/2022] Open
Abstract
Background Distant hybridization between the sea urchin Heliocidaris crassispina (♀) and the sea urchin Strongylocentrotus intermedius (♂) was successfully performed under laboratory conditions. A new variety of hybrid sea urchin (HS hybrid) was obtained. However, the early-development success rates for the HS hybrids were significantly lower than those of purebred H. crassispina or S. intermedius offspring. In addition, it was difficult to distinguish the HS-hybrid adults from the pure H. crassispina adults, which might lead to confusion in subsequent breeding attempts. In this study, we attempted to develop a method to quickly and effectively identify HS hybrids, and to preliminarily investigate the molecular mechanisms underlying the poor early-development success rates in the HS hybrids. Results The hybrid sea urchins (HS hybrids) were identified both morphologically and molecularly. There were no significant differences in the test height to test diameter ratios between the HS hybrids and the parents. The number and arrangement of ambulacral pore pairs in the HS hybrids differed from those of the parental lines, which might serve as a useful morphological character for the identification of the HS hybrids. A primer pair that identified the HS hybrids was screened by comparing the mitochondrial genomes of the parental lines. Moreover, paternal leakage induced mitochondrial DNA heteroplasmy in the HS hybrids, which might explain the low rates of early development success in these hybrids. Conclusions The distant-hybrid sea urchins were accurately identified using comparative morphological and molecular genetic methods. The first evidence of mtDNA heteroplasmy after the distant hybridization of an echinoderm was also provided.
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Doubly Uniparental Inheritance of mtDNA: An Unappreciated Defiance of a General Rule. ADVANCES IN ANATOMY EMBRYOLOGY AND CELL BIOLOGY 2019; 231:25-49. [DOI: 10.1007/102_2018_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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17
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Blanton RE. Population Genetics and Molecular Epidemiology of Eukaryotes. Microbiol Spectr 2018; 6:10.1128/microbiolspec.ame-0002-2018. [PMID: 30387414 PMCID: PMC6217834 DOI: 10.1128/microbiolspec.ame-0002-2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Indexed: 01/16/2023] Open
Abstract
Molecular epidemiology uses the distribution and organization of a pathogen's DNA to understand the distribution and determinants of disease. Since the biology of DNA for eukaryotic pathogens differs substantially from that of bacteria, the analytic approach to their molecular epidemiology can also differ. While many of the genotyping techniques presented earlier in this series, "Advances in Molecular Epidemiology of Infectious Diseases," can be applied to eukaryotes, the output must be interpreted in the light of how DNA is distributed from one generation to the next. In some cases, parasite populations can be evaluated in ways reminiscent of bacteria. They differ, however, when analyzed as sexually reproducing organisms, where all individuals are unique but the genetic composition of the population does not change unless a limited set of events occurs. It is these events (migration, mutation, nonrandom mating, selection, and genetic drift) that are of interest. At a given time, not all of them are likely to be equally important, so the list can easily be narrowed down to understand the driving forces behind the population as it is now and even what it will look like in the future. The main population characteristics measured to assess these events are differentiation and diversity, interpreted in the light of what is known about the population from observation. The population genetics of eukaryotes is important for planning and evaluation of control measures, surveillance, outbreak investigation, and monitoring of the development and spread of drug resistance. *This article is part of a curated collection.
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Affiliation(s)
- Ronald E Blanton
- Center for Global Health & Diseases, Case Western Reserve University, Cleveland, OH 44106
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Meza-Lázaro RN, Poteaux C, Bayona-Vásquez NJ, Branstetter MG, Zaldívar-Riverón A. Extensive mitochondrial heteroplasmy in the neotropical ants of the Ectatomma ruidum complex (Formicidae: Ectatomminae). Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1203-1214. [PMID: 29385929 DOI: 10.1080/24701394.2018.1431228] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts. Heteroplasmy due to hybrid paternal leakage is not supported by phylogenetic analyses. Our results reveal the presence of a fast-evolving secondary mitochondrial lineage of uncertain origin in the E. ruidum complex.
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Affiliation(s)
- Rubi N Meza-Lázaro
- a Colección Nacional de Insectos, Instituto de Biología , Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria , CdMx, México , México
| | - Chantal Poteaux
- b Laboratoire d'Ethologie Expérimentale et Comparée E.A. 4443 (LEEC), Université Paris 13, Sorbonne Paris Cité , Villetaneuse , France
| | | | - Michael G Branstetter
- d USDA-ARS Pollinating Insects Research Unit, Utah State University , Logan , UT , USA
| | - Alejandro Zaldívar-Riverón
- a Colección Nacional de Insectos, Instituto de Biología , Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria , CdMx, México , México
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Foighil DÓ, Smith MJ. EVOLUTION OF ASEXUALITY IN THE COSMOPOLITAN MARINE CLAM LASAEA. Evolution 2017; 49:140-150. [PMID: 28593668 DOI: 10.1111/j.1558-5646.1995.tb05966.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/1992] [Accepted: 06/29/1993] [Indexed: 11/27/2022]
Abstract
The marine clam genus Lasaea is unique among marine bivalves in that it contains both sexual and asexual lineages. We employed molecular tools to infer intrageneric relationships of geographically restricted sexual versus cosmopolitan asexual forms. Polymerase chain reaction primers were used to amplify and sequence homologous 624 nucleotide fragments of COIII from polyploid, asexual, direct-developing individuals representing northeastern Pacific, northeastern Atlantic, Mediterranean, southern Indian Ocean, and Australian populations. DNA sequences also were obtained from the two known diploid congeners, the Australian sexual, indirect developer, Lasaea australis, and an undescribed meiotic Australian direct developer. Estimated tree topologies did not support monophyly for polyploid asexual Lasaea lineages. A robust dichotomy was evident in all phylogenetic trees and each of the two main branches included one of the diploid meitoic Australian congeners. Lasaea australis clustered with two of the direct-developing, polyploid asexual haplotypes, one from Australia, the other from the northeastern Atlantic. Monophyly is supported for the diploid Australian direct-developing lineage together with the remaining polyploid asexual lineages from the northeastern Pacific, northeastern Atlantic, Mediterranean, and southern Indian Ocean. These results indicate that asexual Lasaea lineages are polyphyletic and may have resulted from multiple hybridization events. The high degree of genetic divergence of asexual lineages from co-clustering meiotic congeners (16%-22%) and among geographically restricted monophyletic clones (9%-11%) suggests that asexual Lasaea lineages may be exceptionally long lived.
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Affiliation(s)
- Diarmaid Ó Foighil
- Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
| | - Michael J Smith
- Institute of Molecular Biology and Biochemistry, Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
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Liu H, Mitton JB, Wu S. PATERNAL MITOCHONDRIAL DNA DIFFERENTIATION FAR EXCEEDS MATERNAL MITOCHONDRIAL DNA AND ALLOZYME DIFFERENTIATION IN THE FRESHWATER MUSSEL,
ANODONTA GRANDIS GRANDIS. Evolution 2017; 50:952-957. [DOI: 10.1111/j.1558-5646.1996.tb03907.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/1994] [Accepted: 04/28/1995] [Indexed: 11/29/2022]
Affiliation(s)
- Hsiu‐Ping Liu
- Department of Environmental, Population, Organismic Biology University of Colorado Campus Box 334 Boulder Colorado 80309‐0334
- University of Colorado Museum, Zoology Section Campus Box 315 Boulder Colorado 80309‐0315
| | - Jeffry B. Mitton
- Department of Environmental, Population, Organismic Biology University of Colorado Campus Box 334 Boulder Colorado 80309‐0334
| | - Shi‐Kuei Wu
- University of Colorado Museum, Zoology Section Campus Box 315 Boulder Colorado 80309‐0315
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21
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Next generation sequencing of gonadal transcriptome suggests standard maternal inheritance of mitochondrial DNA in Eurhomalea rufa (Veneridae). Mar Genomics 2017. [DOI: 10.1016/j.margen.2016.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Gusman A, Lecomte S, Stewart DT, Passamonti M, Breton S. Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA. PeerJ 2016; 4:e2760. [PMID: 27994972 PMCID: PMC5157197 DOI: 10.7717/peerj.2760] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 11/05/2016] [Indexed: 11/20/2022] Open
Abstract
There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA) in the animal kingdom: a system named doubly uniparental inheritance (DUI), which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI) in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841)and the veneroid Scrobicularia plana(Da Costa,1778), increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.
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Affiliation(s)
- Arthur Gusman
- Department of Biological Sciences, Université de Montréal , Montréal , Québec , Canada
| | - Sophia Lecomte
- Department of Biological Sciences, Université de Strasbourg , Strasbourg , France
| | - Donald T Stewart
- Department of Biology, Acadia University , Wolfville , Nova Scotia , Canada
| | - Marco Passamonti
- Department of Biological Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal , Montréal , Québec , Canada
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He X, Chen X, Zhang W, Pu Y, Song S, Han J, Dong K, Zhao Q, Guan W, Ma Y, Jiang L. High occurrence of length heteroplasmy in domestic Bactrian camel (Camelus bactrianus). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:851-854. [PMID: 27937010 DOI: 10.1080/24701394.2016.1197219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Heteroplasmy is the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual. In this study, sequence variation was investigated in the control region (CR) of mitochondrial DNA (mtDNA) from 135 individuals belonging to five primary domestic Bactrian camel breeds in China and Mongolia. Due to variation of the repeat unit G(T/C)(AC)n, length heteroplasmy was detected within each camel by direct sequencing and fragment analysis. A high occurrence of mtDNA heteroplasmy, up to 100 percentages was observed in five camel populations. Our study provides the first evidence of extensive length heteroplasmy in Bactrian camels.
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Affiliation(s)
- Xiaohong He
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Xiaofei Chen
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Wenbin Zhang
- c Bactrian Camels Institute of Alxa League , Inner Mongolia Autonomous Region , China
| | - Yabin Pu
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Shen Song
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Jianlin Han
- b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,d International Livestock Research Institute (ILRI) , Nairobi , Kenya
| | - Kunzhe Dong
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Qianjun Zhao
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Weijun Guan
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Yuehui Ma
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
| | - Lin Jiang
- a The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China.,b CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources , Institute of Animal Science, Chinese Academy of Agricultural Science (CAAS) , Beijing , China
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Pierszalowski SP, Gabriele CM, Steel DJ, Neilson JL, Vanselow PBS, Cedarleaf JA, Straley JM, Baker CS. Local recruitment of humpback whales in Glacier Bay and Icy Strait, Alaska, over 30 years. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Trovant B, Basso NG, Orensanz JM, Lessa EP, Dincao F, Ruzzante DE. Scorched mussels (Brachidontes spp., Bivalvia: Mytilidae) from the tropical and warm-temperate southwestern Atlantic: the role of the Amazon River in their speciation. Ecol Evol 2016; 6:1778-98. [PMID: 26929816 PMCID: PMC4758806 DOI: 10.1002/ece3.2016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 11/16/2022] Open
Abstract
Antitropicality is a distribution pattern where closely related taxa are separated by an intertropical latitudinal gap. Two potential examples include Brachidontes darwinianus (south eastern Brazil to Uruguay), considered by some authors as a synonym of B. exustus (Gulf of Mexico and the Caribbean), and B. solisianus, distributed along the Brazilian coast with dubious records north of the intertropical zone. Using two nuclear (18S and 28S rDNA) and one mitochondrial gene (mtDNA COI), we aimed to elucidate the phylogeographic and phylogenetic relationships among the scorched mussels present in the warm-temperate region of the southwest Atlantic. We evaluated a divergence process mediated by the tropical zone over alternative phylogeographic hypotheses. Brachidontes solisianus was closely related to B. exustus I, a species with which it exhibits an antitropical distribution. Their divergence time was approximately 2.6 Ma, consistent with the intensification of Amazon River flow. Brachidontes darwinianus, an estuarine species is shown here not to be related to this B. exustus complex. We suspect ancestral forms may have dispersed from the Caribbean to the Atlantic coast via the Trans-Amazonian seaway (Miocene). The third species, B rodriguezii is presumed to have a long history in the region with related fossil forms going back to the Miocene. Although scorched mussels are very similar in appearance, their evolutionary histories are very different, involving major historical contingencies as the formation of the Amazon River, the Panama Isthmus, and the last marine transgression.
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Affiliation(s)
- Berenice Trovant
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Néstor G. Basso
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - José María Orensanz
- Instituto de Diversidad y Evolución (IDEAus‐CONICET)Boulevard Brown 2915U9120ACFPuerto MadrynChubutArgentina
| | - Enrique P. Lessa
- Departamento de Ecología y EvoluciónFacultad de CienciasUniversidad de la RepúblicaIguá 4225C.P. 11400MontevideoUruguay
| | - Fernando Dincao
- Universidade Federal do Rio Grande – FURGAv. Itália km 8 Bairro Carreiros96203‐900Rio GrandeBrazil
| | - Daniel E. Ruzzante
- Department of BiologyDalhousie University1355 Oxford St.HalifaxNova ScotiaB3H 4R2Canada
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Mohrbeck I, Raupach MJ, Martínez Arbizu P, Knebelsberger T, Laakmann S. High-Throughput Sequencing-The Key to Rapid Biodiversity Assessment of Marine Metazoa? PLoS One 2015; 10:e0140342. [PMID: 26479071 PMCID: PMC4610693 DOI: 10.1371/journal.pone.0140342] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 09/24/2015] [Indexed: 02/03/2023] Open
Abstract
The applications of traditional morphological and molecular methods for species identification are greatly restricted by processing speed and on a regional or greater scale are generally considered unfeasible. In this context, high-throughput sequencing, or metagenetics, has been proposed as an efficient tool to document biodiversity. Here we evaluated the effectiveness of 454 pyrosequencing in marine metazoan community analysis using the 18S rDNA: V1-V2 region. Multiplex pyrosequencing of the V1-V2 region was used to analyze two pooled samples of DNA, one comprising 118 and the other 37 morphologically identified species, and one natural sample taken directly from a North Sea zooplankton community. A DNA reference library comprising all species represented in the pooled samples was created by Sanger sequencing, and this was then used to determine the optimal similarity threshold for species delineation. The optimal threshold was found at 99% species similarity, with 85% identification success. Pyrosequencing was able to identify between fewer species: 67% and 78% of the species in the two pooled samples. Also, a large number of sequences for three species that were not included in the pooled samples were amplified by pyrosequencing, suggesting preferential amplification of some genotypes and the sensitivity of this approach to even low levels of contamination. Conversely, metagenetic analysis of the natural zooplankton sample identified many more species (particularly gelatinous zooplankton and meroplankton) than morphological analysis of a formalin-fixed sample from the same sampling site, suggesting an increased level of taxonomic resolution with pyrosequencing. The study demonstrated that, based on the V1-V2 region, 454 sequencing does not provide accurate species differentiation and reliable taxonomic classification, as it is required in most biodiversity monitoring. The analysis of artificially prepared samples indicated that species detection in pyrosequencing datasets is complicated by potential PCR-based biases and that the V1-V2 marker is poorly resolved for some taxa.
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Affiliation(s)
- Inga Mohrbeck
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Michael J Raupach
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Pedro Martínez Arbizu
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Thomas Knebelsberger
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
| | - Silke Laakmann
- Department German Center for Marine Biodiversity Research, Senckenberg am Meer, Wilhelmshaven, Germany
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Barco A, Raupach MJ, Laakmann S, Neumann H, Knebelsberger T. Identification of North Sea molluscs with DNA barcoding. Mol Ecol Resour 2015; 16:288-97. [DOI: 10.1111/1755-0998.12440] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/09/2015] [Accepted: 06/17/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Andrea Barco
- GEOMAR-Helmholtz Centre for Ocean Research Kiel; Düsternbrooker Weg 20 24105 Kiel Germany
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Michael J. Raupach
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Silke Laakmann
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Hermann Neumann
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
| | - Thomas Knebelsberger
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Südstrand 44 26382 Wilhelmshaven Germany
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Vargas J, Pérez M, Toro J, Astorga MP. Presence of two mitochondrial genomes in the mytilid Perumytilus purpuratus: Phylogenetic evidence for doubly uniparental inheritance. Genet Mol Biol 2015; 38:173-81. [PMID: 26273220 PMCID: PMC4530645 DOI: 10.1590/s1415-47573822201420140262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 01/22/2015] [Indexed: 11/24/2022] Open
Abstract
This study presents evidence, using sequences of ribosomal 16S and COI mtDNA, for the presence of two mitochondrial genomes in Perumytilus purpuratus. This may be considered evidence of doubly uniparental mtDNA inheritance. The presence of the two types of mitochondrial genomes differentiates females from males. The F genome was found in the somatic and gonadal tissues of females and in the somatic tissues of males; the M genome was found in the gonads and mantle of males only. For the mitochondrial 16S region, ten haplotypes were found for the F genome (nucleotide diversity 0.004), and 7 haplotypes for the M genome (nucleotide diversity 0.001), with a distance Dxy of 0.125 and divergence Kxy of 60.33%. For the COI gene 17 haplotypes were found for the F genome (nucleotide diversity 0.009), and 10 haplotypes for the M genome (nucleotide diversity 0.010), with a genetic distance Dxy of 0.184 and divergence Kxy of 99.97%. Our results report the presence of two well-differentiated, sex-specific types of mitochondrial genome (one present in the male gonad, the other in the female gonad), implying the presence of DUI in P. purpuratus. These results indicate that care must be taken in phylogenetic comparisons using mtDNA sequences of P. purpuratus without considering the sex of the individuals.
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Affiliation(s)
- Jaime Vargas
- Instituto de Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile
| | - Montse Pérez
- > Instituto Español de Oceanografía. Centro Oceanográfico de Vigo, Vigo, Spain
| | - Jorge Toro
- Instituto de Ciencias Marinas y Limnológicas. Universidad Austral de Chile, Valdivia, Chile
| | - Marcela P Astorga
- Instituto de Acuicultura, Universidad Austral de Chile, Puerto Montt, Chile
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Song H, Moulton MJ, Whiting MF. Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta). PLoS One 2014; 9:e110508. [PMID: 25333882 PMCID: PMC4204883 DOI: 10.1371/journal.pone.0110508] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 02/06/2023] Open
Abstract
Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.
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Affiliation(s)
- Hojun Song
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Matthew J. Moulton
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Museum, Brigham Young University, Provo, Utah, United States of America
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30
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Chitwood JL, Rincon G, Kaiser GG, Medrano JF, Ross PJ. RNA-seq analysis of single bovine blastocysts. BMC Genomics 2013; 14:350. [PMID: 23705625 PMCID: PMC3668197 DOI: 10.1186/1471-2164-14-350] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 05/14/2013] [Indexed: 11/22/2022] Open
Abstract
Background Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect. Results We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. Conclusions This study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression.
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Affiliation(s)
- James L Chitwood
- Department of Animal Science, University of California, Davis, Davis, CA, USA
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31
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Song H, Moulton MJ, Hiatt KD, Whiting MF. Uncovering historical signature of mitochondrial DNA hidden in the nuclear genome: the biogeography ofSchistocercarevisited. Cladistics 2013; 29:643-662. [DOI: 10.1111/cla.12013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Hojun Song
- Department of Biology; University of Central Florida; Orlando FL 32816 USA
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Matthew J. Moulton
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Kevin D. Hiatt
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
| | - Michael F. Whiting
- Department of Biology and M. L. Bean Life Science Museum; Brigham Young University; Provo UT 84602 USA
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32
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Biparental Inheritance Through Uniparental Transmission: The Doubly Uniparental Inheritance (DUI) of Mitochondrial DNA. Evol Biol 2012. [DOI: 10.1007/s11692-012-9195-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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33
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Affiliation(s)
- David P L Toews
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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34
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Breton S, Stewart DT, Shepardson S, Trdan RJ, Bogan AE, Chapman EG, Ruminas AJ, Piontkivska H, Hoeh WR. Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)? Mol Biol Evol 2011; 28:1645-59. [PMID: 21172831 PMCID: PMC3107663 DOI: 10.1093/molbev/msq345] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial (mt) function depends critically on optimal interactions between components encoded by mt and nuclear DNAs. mitochondrial DNA (mtDNA) inheritance (SMI) is thought to have evolved in animal species to maintain mito-nuclear complementarity by preventing the spread of selfish mt elements thus typically rendering mtDNA heteroplasmy evolutionarily ephemeral. Here, we show that mtDNA intraorganismal heteroplasmy can have deterministic underpinnings and persist for hundreds of millions of years. We demonstrate that the only exception to SMI in the animal kingdom, that is, the doubly uniparental mtDNA inheritance system in bivalves, with its three-way interactions among egg mt-, sperm mt- and nucleus-encoded gene products, is tightly associated with the maintenance of separate male and female sexes (dioecy) in freshwater mussels. Specifically, this mother-through-daughter and father-through-son mtDNA inheritance system, containing highly differentiated mt genomes, is found in all dioecious freshwater mussel species. Conversely, all hermaphroditic species lack the paternally transmitted mtDNA (=possess SMI) and have heterogeneous macromutations in the recently discovered, novel protein-coding gene (F-orf) in their maternally transmitted mt genomes. Using immunoelectron microscopy, we have localized the F-open reading frame (ORF) protein, likely involved in specifying separate sexes, in mitochondria and in the nucleus. Our results support the hypothesis that proteins coded by the highly divergent maternally and paternally transmitted mt genomes could be directly involved in sex determination in freshwater mussels. Concomitantly, our study demonstrates novel features for animal mt genomes: the existence of additional, lineage-specific, mtDNA-encoded proteins with functional significance and the involvement of mtDNA-encoded proteins in extra-mt functions. Our results open new avenues for the identification, characterization, and functional analyses of ORFs in the intergenic regions, previously defined as "noncoding," found in a large proportion of animal mt genomes.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, Kent State University, Kent, OH, USA.
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Abstract
More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.
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Affiliation(s)
- Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
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36
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Kuroiwa T. Review of cytological studies on cellular and molecular mechanisms of uniparental (maternal or paternal) inheritance of plastid and mitochondrial genomes induced by active digestion of organelle nuclei (nucleoids). JOURNAL OF PLANT RESEARCH 2010; 123:207-230. [PMID: 20145972 DOI: 10.1007/s10265-009-0306-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 12/07/2009] [Indexed: 05/28/2023]
Abstract
In most sexual organisms, including isogamous, anisogamous and oogamous organisms, uniparental transmission is a striking and universal characteristic of the transmission of organelle (plastid and mitochondrial) genomes (DNA). Using genetic, biochemical and molecular biological techniques, mechanisms of uniparental (maternal and parental) and biparental transmission of organelle genomes have been studied and reviewed. Although to date there has been no cytological review of the transmission of organelle genomes, cytology offers advantages in terms of direct evidence and can enhance global studies of the transmission of organelle genomes. In this review, I focus on the cytological mechanism of uniparental inheritance by "active digestion of male or female organelle nuclei (nucleoids, DNA)" which is universal among isogamous, anisogamous, and oogamous organisms. The global existence of uniparental transmission since the evolution of sexual eukaryotes may imply that the cell nuclear genome continues to inhibit quantitative evolution of organelles by organelle recombination.
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Affiliation(s)
- Tsuneyoshi Kuroiwa
- Research Information Center for Extremophile, Graduate School of Science, Rikkyo University, Tokyo 171-8501, Japan.
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37
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Buckland-Nicks J, Schander C. Fertilization in the white chiton, Stenosemus albus, with implications for its phylogenetic position. CAN J ZOOL 2008. [DOI: 10.1139/z08-082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gamete structure and fertilization biology of the white chiton, Stenosemus albus (L., 1767), were studied with light and electron microscopy. Sperm structure was found to be similar to other Chitonina, but acrosomes are homogeneous in this species, like those of Chaetopleura apiculata (Say in Conrad, 1834). The egg of S. albus is covered by long spines with hooked tips. The bases of spines are perforated along their perimeters by a series of pores that provide sperm with direct access to the vitelline layer. This feature appears to be plesiomorphic and characterizes also Chaetopleura but not most Chitonina, which have a continuous dense layer overlying the hull. Beneath the vitelline layer, the egg membrane is formed into a series of cups with raised edges elaborated into microvilli that coincide with the bases of hull spines. Free-spawned sperm of S. albus were able to find the egg and penetrate a pore in the hull within 20 s. Evidence presented here, and previously, indicates that S. albus shares a number of key characters in common with Callochitonidae, which is a basal family within Chitonida. Taken together, the evidence suggests that Stenosemus belongs to a basal taxon within Chitonina, outside the Ischnochitoninae, in which it is currently placed.
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Affiliation(s)
- J. Buckland-Nicks
- Department of Biology, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada
- University of Bergen, P.O. Box 7800, Bergen N-5020, Norway
| | - C. Schander
- Department of Biology, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada
- University of Bergen, P.O. Box 7800, Bergen N-5020, Norway
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38
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Buckland-Nicks J, Brothers E. On fertilization in Chaetopleura apiculata and selected Chitonida. THE BIOLOGICAL BULLETIN 2008; 214:184-193. [PMID: 18401000 DOI: 10.2307/25066675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Early events of fertilization are described in Chaetopleura apiculata and other selected Chitonida. C. apiculata egg hulls are elaborated into multi-branched spines with interlocking polygonal bases. Around the perimeter of each base are a series of open pores, ranging in size from 0.1-0.5 microm, which permit sperm direct access to the vitelline layer. In Callochitonidae (Chitonida) even larger pores occur in egg jelly coats, but this is considered to be the plesiomorphic condition, found also in Lepidopleurida such as Deshayesiella curvata. Other Chitonina, such as Rhyssoplax tulipa and Acanthopleura granulata, have a continuous outer dense layer that lacks pores and must be digested by penetrating sperm. Fertilization in Chitonida is unique and involves injection of chromatin into the egg via a narrow tubular nuclear extension that appears to exclude other sperm organelles, including mitochondria, centrioles, and flagellum. New evidence from studies of fertilization in Mopalia muscosa (Chitonida: Acanthochitonina) supports this hypothesis. This type of fertilization implies maternal inheritance of both mitochondria and centrioles, which is highly unusual, because in most animals one sperm centriole assists movements of pronuclei and regulates organization of the mitotic spindle. This mechanism of fertilization is defined by a series of apomorphic characters that unify the order Chitonida.
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39
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Breton S, Beaupré HD, Stewart DT, Hoeh WR, Blier PU. The unusual system of doubly uniparental inheritance of mtDNA: isn't one enough? Trends Genet 2007; 23:465-74. [PMID: 17681397 DOI: 10.1016/j.tig.2007.05.011] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 05/24/2007] [Indexed: 10/23/2022]
Abstract
Mitochondria possess their own genetic material (mitochondrial DNA or mtDNA), whose gene products are involved in mitochondrial respiration and oxidative phosphorylation, transcription, and translation. In animals, mitochondrial DNA is typically transmitted to offspring by the mother alone. The discovery of 'doubly uniparental inheritance' (DUI) of mtDNA in some bivalves has challenged the paradigm of strict maternal inheritance (SMI). In this review, we survey recent advances in our understanding of DUI, which is a peculiar system of cytoplasmic DNA inheritance that involves distinct maternal and paternal routes of mtDNA transmission, a novel extension of a mitochondrial gene (cox2), recombination, and periodic 'role-reversals' of the normally male and female-transmitted mitochondrial genomes. DUI provides a unique opportunity for studying nuclear-cytoplasmic genome interactions and the evolutionary significance of different modes of mitochondrial inheritance.
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Affiliation(s)
- Sophie Breton
- Département de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Québec, G5L 3A1, Canada.
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40
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Songram O, Sittipraneed S, Klinbunga S. Mitochondrial DNA diversity and genetic differentiation of the honeybee (Apis cerana) in Thailand. Biochem Genet 2006; 44:256-69. [PMID: 17028787 DOI: 10.1007/s10528-006-9030-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Accepted: 10/13/2005] [Indexed: 11/26/2022]
Abstract
Genetic diversity of the honeybee (Apis cerana) in Thailand collected from north, northeast, the central region, peninsular Thailand, and Samui Island (n = 181) was examined by PCR-RFLP of ATPase6-ATPase8. Interestingly, 78 individuals (43.09%) of the southern-latitude bees exhibited length heteroplasmy of the PCR product. The gel-eluted ATPase6-ATPase8 (825 bp) of each bee was restricted with TaqI, SspI, and VspI, respectively. Eight mitotypes were generated and revealed biogeographic differentiation between conspecific samples of A. cerana. AAA, ACA, AAD, BAA, ADA, and ABA were found only in the north-to-central samples (north, northeast, and central region); BBB and BBC were found in the southern-latitude bees; and BBC was restrictively found in the Samui sample. Large genetic distances were observed between each of the north-to-central samples and peninsular Thailand and Samui samples, but lower levels of genetic distance were found within each region. Geographic heterogeneity and phylogenetic analyses indicated that Thai A. cerana could be genetically differentiated into northern Thailand, peninsular Thailand, and Samui Island populations.
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Affiliation(s)
- Onuma Songram
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10300, Thailand
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41
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Walther AC, Lee T, Burch JB, Foighil DO. E Pluribus Unum: A phylogenetic and phylogeographic reassessment of Laevapex (Pulmonata: Ancylidae), a North American genus of freshwater limpets. Mol Phylogenet Evol 2006; 40:501-16. [PMID: 16678447 DOI: 10.1016/j.ympev.2006.03.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 01/04/2006] [Accepted: 03/15/2006] [Indexed: 11/25/2022]
Abstract
The North American freshwater limpet genus Laevapex (Walker, 1903) is a ubiquitous inhabitant of lentic and slow-moving lotic habitats east of the Rocky Mountains, but uncertainty clouds its systematic affinities, the phylogenetic validity of its constituent nominal species, and its degree of genetic connectivity among drainages. We addressed these issues by sampling the genus throughout much of its collective range and constructing representative nuclear and mitochondrial (mt) gene trees, in addition to performing morphometric analyses of shell shape variation. Our results identify neotropical Gundlachia and South American Uncancylus as sister lineages for Laevapex and reveal a pronounced sub-familial dichotomy within the Ancylidae, separating these three New World genera from a Holarctic (Ferrissia (Ancylus, Rhodacmea)) sister clade. Five nominal taxa (L. fuscus, L. diaphanus, L. peninsulae, L. sp., and "F."arkansasensis), indistinguishable in our morphometric analyses, were polyphyletic in the mt gene trees, exhibited modest levels (< 3.9%) of genetic divergence in the primary (103 of 109 individuals) mt clade and, with one minor exception, they appeared fixed for a single nuclear ITS-2 genotype. Although complicated by the presence of rare, highly divergent mt lineages (of either introgressive or persistent ancestral polymorphic origin) in some populations, the molecular data were consistent with a taxonomic conclusion that these five nominal taxa represent a single polymorphic lineage of the type species L. fuscus. AMOVA analyses indicated that 56% of the observed mt variation could be attributed to among population differences, only two of 36 haplotypes were detected in more than one sampling location, and estimates of among-population mt gene flow were generally low at both regional and continental scales. Unrooted network analyses revealed a number of mt tip clades, one restricted to the southwestern part of the range, the remainder having overlapping distributions in eastern North America. All of the eastern tip clades occurred in the Mid-Atlantic region, and these samples displayed by far the highest levels of collective mt diversity. However, directional gene flow estimates indicated that this region has been a recipient (especially from Alabama populations), rather than a source of haplotypic diversity, implying that it likely represents a center of overlap, not a primary ice age refugium, for this limpet species.
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Affiliation(s)
- Andrea C Walther
- Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1079, USA.
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42
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Breton S, Burger G, Stewart DT, Blier PU. Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels (Mytilus spp.). Genetics 2005; 172:1107-19. [PMID: 16322521 PMCID: PMC1456209 DOI: 10.1534/genetics.105.047159] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine mussels of the genus Mytilus have an unusual mode of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Female mussels are homoplasmic for the F mitotype, which is inherited maternally, while males are usually heteroplasmic, carrying a mixture of the maternal F mitotype and the paternally inherited M genome. Two classes of M genomes have been observed: "standard" M genomes and "recently masculinized" M genomes. The latter are more similar to F genomes at the sequence level but are transmitted paternally like standard M genomes. In this study we report the complete sequences of two standard male M. edulis and one recently masculinized male M. trossulus mitochondrial genome. A comparative analysis, including the previously sequenced M. edulis F and M. galloprovincialis F and M mtDNAs, reveals that these genomes are identical in gene order, but highly divergent in nucleotide and amino acid sequence. The large amount (>20%) of nucleotide substitutions that fall in coding regions implies that there are several amino acid replacements between the F and M genomes, which likely have an impact on the structural and functional properties of the mitochondrial proteome. Correlation of the divergence rate of different protein-coding genes indicates that mtDNA-encoded proteins of the M genome are still under selective constraints, although less highly than genes of the F genome. The mosaic F/M control region of the masculinized F genome provides evidence for lineage-specific sequences that may be responsible for the different mode of transmission genetics. This analysis shows the value of comparative genomics to better understand the mechanisms of maintenance and segregation of mtDNA sequence variants in mytilid mussels.
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Affiliation(s)
- Sophie Breton
- Laboratoire de Biologie Evolutive, Département de Biologie, Université du Quebec, Rimouski, Canada
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43
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Oshaghi MA. mtDNA inheritance in the mosquitoes of Anopheles stephensi. Mitochondrion 2005; 5:266-71. [PMID: 16050989 DOI: 10.1016/j.mito.2005.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 05/04/2005] [Accepted: 05/06/2005] [Indexed: 11/24/2022]
Abstract
The inheritance of mtDNA was tested in malaria vector mosquitoes of Anopheles stephensi strains using PCR-RFLP analysis for its utility in addressing epidemiological questions related to the transmission and spread of malaria. Reciprocal crosses were made between two haplotypes with distinct mtDNA restriction fragment length polymorphism (RFLP) profiles through 20 consecutive generations. All of the progenies produced by these crosses had the mtDNA haplotype of the female parent suggesting that, if it occurs, paternal inheritance of mtDNA in An. stephensi is rare.
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Affiliation(s)
- Mohammad A Oshaghi
- Department of Medical Entomology, Tehran School of Public Health and Institute of Health Researches, Tehran University of Medical Sciences, P.O. Box 6446, Tehran 14155, Iran.
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44
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Curole JP, Kocher TD. Evolution of a Unique Mitotype-Specific Protein-Coding Extension of the Cytochrome c Oxidase II Gene in Freshwater Mussels (Bivalvia: Unionoida). J Mol Evol 2005; 61:381-9. [PMID: 16082567 DOI: 10.1007/s00239-004-0192-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2004] [Accepted: 03/10/2005] [Indexed: 11/25/2022]
Abstract
A unique mode of mitochondrial DNA inheritance, designated doubly-uniparental inheritance (DUI), occurs in three bivalve subclasses (Pteriomorpha: Mytiloida, Palaeoheterodonta: Unionoida, Heterodonta: Veneroida), indicating that DUI may be a widespread phenomenon among bivalves. In mytiloids, breakdown of this pattern of inheritance (gender-switching) is observed in natural populations and in a phylogenetic context. In contrast, gender-switching has not occurred during the evolutionary history of unionoids. Here we present sequences for the male (M) and female (F) mitotypes from an additional 8 species of Unionoida. Consistent with previous observations, the M and F mitotypes of all species form reciprocally monophyletic clades supporting the hypothesis of taxon-specific rates of gender-switching. Coinciding with the absence of gender-switching is an approximately 185 codon extension of the cytochrome c oxidase II (MTCO2) locus in the male genome. The extension is present in all 12 unionoid species examined, including a representative of the family Margaritiferidae, indicating that this protein-coding polymorphism originated > or = 200 MYBP: . Although the extension is well conserved in length among 11 of the 12 species, one taxon has a significantly shortened extension. Lastly, examination of the rates and patterns of substitution indicate that the extension is evolving under relaxed purging selection, a pattern inconsistent with the conserved nature of MTCO2 or any cytochrome c oxidase locus.
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Affiliation(s)
- Jason P Curole
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, 03824, USA.
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St John JC, Schatten G. Paternal mitochondrial DNA transmission during nonhuman primate nuclear transfer. Genetics 2005; 167:897-905. [PMID: 15238538 PMCID: PMC1470892 DOI: 10.1534/genetics.103.025049] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Offspring produced by nuclear transfer (NT) have identical nuclear DNA (nDNA). However, mitochondrial DNA (mtDNA) inheritance could vary considerably. In sheep, homoplasmy is maintained since mtDNA is transmitted from the oocyte (recipient) only. In contrast, cattle are heteroplasmic, harboring a predominance of recipient mtDNA along with varying levels of donor mtDNA. We show that the two nonhuman primate Macaca mulatta offspring born by NT have mtDNA from three sources: (1) maternal mtDNA from the recipient egg, (2) maternal mtDNA from the egg contributing to the donor blastomere, and (3) paternal mtDNA from the sperm that fertilized the egg from which the donor blastomere was isolated. The introduction of foreign mtDNA into reconstructed recipient eggs has also been demonstrated in mice through pronuclear injection and in humans through cytoplasmic transfer. The mitochondrial triplasmy following M. mulatta NT reported here forces concerns regarding the parental origins of mtDNA in clinically reconstructed eggs. In addition, mtDNA heteroplasmy might result in the embryonic stem cell lines generated for experimental and therapeutic purposes ("therapeutic cloning").
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Affiliation(s)
- Justin C St John
- Mitochondrial and Reproductive Genetics Group, Division of Medical Sciences, University of Birmingham, Birmingham B15 2TH, United Kingdom
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Abstract
Summary Human mitochondrial DNA (mtDNA) encodes 13 of the polypeptides associated with the process of oxidative phosphorylation (OXPHOS), the cells most important ATP generating pathway. Until recently, the effects of mtDNA rearrangements on male fertility have been largely ignored. However, it is becoming increasingly evident that both point mutations and large-scale deletions may have an impact on sperm motility and morphology. We discuss the implications of these rearrangements in the context of the clinical setting. We further discuss the possible consequences resulting from the transmission of sperm mtDNA deletions to the offspring. The role of nucleo-cytoplasmic interaction is investigated in the context of nuclear transcription and replication factors that regulate mtDNA transcription and replication.
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Affiliation(s)
- Justin C St John
- The University of Birmingham, The Division of Medical Sciences, Birmingham B15 2TJ, UK.
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Nagashima K, Sato M, Kawamata K, Nakamura A, Ohta T. Genetic structure of Japanese scallop population in Hokkaido, analyzed by mitochondrial haplotype distribution. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2005; 7:1-10. [PMID: 15806334 DOI: 10.1007/s10126-004-3046-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2003] [Accepted: 04/30/2004] [Indexed: 05/24/2023]
Abstract
To examine the genetic structure of Japanese scallop populations (Mizuhopecten yessoensis) in Hokkaido prefecture, Japan, and compare it with those in the Aomori prefecture, we applied a method for lineage analysis based on sequence variation in a mitochondrial DNA segment (NcR2). After showing that there was a low probability of doubly uniparental inheritance of mitochondrial DNA in the scallop, we sequenced the NcR2 regions of 914 individuals from 15 populations (13 in Hokkaido and 2 in Aomori). In total, 103 different haplotypes were detected. Results of homogeneity tests for pairwise populations and the fixation indices indicated that significant heterogeneity (P < 0.0005) and structuring (pairwise fixation index F(ST) = 0.1606-0.4444, P = 0.0000; fixation index among groups F(CT) = 0.1549, P = 0.0078) could be inferred between the Hokkaido and Aomori groups, but not among populations within the groups. Moreover, heterogeneity of the haplotype distribution between populations of the 1980s and 1990s or 2000s at the 4 culturing areas was not observed (P > 0.05), and the haplotype diversity between them was not significant (P = 0.05), suggesting that the culture operations had not imparted a significant effect on the genetic structure during these periods.
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Affiliation(s)
- Koji Nagashima
- Hokkaido Food Processing Research Center, 589-4 Bunkyodai-midorimachi, Ebetsu, Hokkaido 069-0836, Japan.
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Lee T, Foighil DO. Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex. Mol Ecol 2004; 13:3527-42. [PMID: 15488009 DOI: 10.1111/j.1365-294x.2004.02337.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The well-documented Floridian 'Gulf/Atlantic' marine genetic disjunction provides an influential example of vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. We are engaged in a two-part study that aims to place this disjunction into a regional Caribbean Basin phylogenetic perspective using the scorched mussel Brachidontes exustus as an exemplar. Our first step, documented here, is to thoroughly characterize the genetic structure of Floridian scorched mussel populations using mitochondrial (mt) and nuclear markers. Both sets of markers recovered the expected disjunction involving sister clades distributed on alternate flanks of peninsular Florida and lineage-specific mt molecular clocks placed its origin in the Pliocene. The two sister clades had distinct population genetic profiles and the Atlantic clade appears to have experienced an evolutionarily recent bottleneck, although plots of the relative estimates of N through time are consistent with its local persistence through the last Ice Age Maximum. Our primary novel result, however, was the discovery that the Gulf/Atlantic disjunction represents but one of three cryptic, nested genetic discontinuities represented in Floridian scorched mussel populations. The most pronounced phylogenetic split distinguished the Gulf and Atlantic sister clades from two additional nested cryptic sister clades present in samples taken from the southern Florida tropical marine zone. Floridian populations of B. exustus are composed of four cryptic taxa, a result consistent with the hypothesis that the Gulf/Atlantic disjunction in this morphospecies is but one of multiple latent regional genetic breakpoints.
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Affiliation(s)
- T Lee
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA.
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St John JC, Lloyd REI, Bowles EJ, Thomas EC, El Shourbagy S. The consequences of nuclear transfer for mammalian foetal development and offspring survival. A mitochondrial DNA perspective. Reproduction 2004; 127:631-41. [PMID: 15175500 DOI: 10.1530/rep.1.00138] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The introduction of nuclear transfer (NT) and other technologies that involve embryo reconstruction require us to reinvestigate patterns of mitochondrial DNA (mtDNA) transmission, transcription and replication. MtDNA is a 16.6 kb genome located within each mitochondrion. The number of mitochondria and mtDNA copies per organelle is specific to each cell type. MtDNA is normally transmitted through the oocyte to the offspring. However, reconstructed oocytes often transmit both recipient oocyte mtDNA and mtDNA associated with the donor nucleus. We argue that the transmission of two populations of mtDNA may have implications for offspring survival as only one allele might be actively transcribed. This could result in the offspring phenotypically exhibiting mtDNA depletion-type syndromes. A similar occurrence could arise when nucleo-cytoplasmic interactions fail to regulate mtDNA transcription and replication, especially as the initiation of mtDNA replication post-implantation is a key developmental event. Furthermore, failure of the donor somatic nucleus to be reprogrammed could result in the early initiation of replication and the loss of cellular mtDNA specificity. We suggest investigations should be conducted to enhance our understanding of nucleo-cytoplasmic interactions in order to improve NT efficiency.
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Affiliation(s)
- Justin C St John
- The Mitochondrial and Reproductive Genetics Group, The Division of Medical Sciences, The Medical School, The University of Birmingham, Birmingham B15 2TT, UK.
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Quesada H, Stuckas H, Skibinski DOF. Heteroplasmy suggests paternal co-transmission of multiple genomes and pervasive reversion of maternally into paternally transmitted genomes of mussel (Mytilus) mitochondrial DNA. J Mol Evol 2004; 57 Suppl 1:S138-47. [PMID: 15008410 DOI: 10.1007/s00239-003-0019-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Marine mussels of the genus Mytilus have two types of mitochondrial DNA with separate paternal and maternal inheritance. Females are homoplasmic for an F genome that is transmitted to all offspring, whereas males are heteroplasmic for this F genome and for a highly diverged (> 20%) M genome that is transmitted only to sons. Here we provide phylogenetic evidence based on lrRNA sequence data that most of the paternal genomes in European M. trossulus have an introgressive female M. edulis origin and are nearly indistinguishable in sequence from F types of M. trossulus. This observation is best explained by the hypothesis that introgressed F type molecules have recently invaded the paternal route and have assumed the role of M molecules, then resetting to zero the time of sequence divergence between M and F lineages. European M. trossulus shows a high prevalence of males heteroplasmic for three different mitochondrial DNA types all having the same two paternal types and the same maternal type, consistent with paternal co-transmission of multiple genomes. Co-transmission of the same genomes must apparently operate uninterruptedly for several generations in spite of the very different evolutionary origin of the specific molecules that are transmitted paternally and maternally in European M. trossulus.
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Affiliation(s)
- Humberto Quesada
- School of Biological Sciences, University of Wales, Swansea, Swansea SA2 8PP, United Kingdom.
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