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Choi SS, Mc Cartney A, Park D, Roberts H, Brav-Cubitt T, Mitchell C, Buckley TR. Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects. Mol Ecol 2024:e17422. [PMID: 38842022 DOI: 10.1111/mec.17422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/03/2024] [Accepted: 04/17/2024] [Indexed: 06/07/2024]
Abstract
During hybrid speciation, homoeologues combine in a single genome. Homoeologue expression bias (HEB) occurs when one homoeologue has higher gene expression than another. HEB has been well characterized in plants but rarely investigated in animals, especially invertebrates. Consequently, we have little idea as to the role that HEB plays in allopolyploid invertebrate genomes. If HEB is constrained by features of the parental genomes, then we predict repeated evolution of similar HEB patterns among hybrid genomes formed from the same parental lineages. To address this, we reconstructed the history of hybridization between the New Zealand stick insect genera Acanthoxyla and Clitarchus using a high-quality genome assembly from Clitarchus hookeri to call variants and phase alleles. These analyses revealed the formation of three independent diploid and triploid hybrid lineages between these genera. RNA sequencing revealed a similar magnitude and direction of HEB among these hybrid lineages, and we observed that many enriched functions and pathways were also shared among lineages, consistent with repeated evolution due to parental genome constraints. In most hybrid lineages, a slight majority of the genes involved in mitochondrial function showed HEB towards the maternal homoeologues, consistent with only weak effects of mitonuclear incompatibility. We also observed a proteasome functional enrichment in most lineages and hypothesize this may result from the need to maintain proteostasis in hybrid genomes. Reference bias was a pervasive problem, and we caution against relying on HEB estimates from a single parental reference genome.
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Affiliation(s)
- Seung-Sub Choi
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Ann Mc Cartney
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Duckchul Park
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Hester Roberts
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
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Chu H, Cui C, Su X, Zhang H, Ma J, Zhu H, Bai L, Li R. Research progress in mitochondrial quality control in schizophrenia. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2024; 49:128-134. [PMID: 38615174 PMCID: PMC11017019 DOI: 10.11817/j.issn.1672-7347.2024.230398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Indexed: 04/15/2024]
Abstract
Mitochondria are the main site of energy metabolism within cells, generating a substantial amount of ATP to supply energy to the human body. Research has shown that alterations in mitochondrial structure and function exist in individuals with schizophrenia, suggesting their potential impact on the onset of psychiatric disorders and clinical treatment efficacy. Therefore, understanding the research progress on the genetic mechanisms, pathological processes, image manifestations of schizophrenia and mitochondrial quality control, and summarizing the relevant evidence of mitochondrial-related targets as potential therapeutic targets for schizophrenia, can provide references for further research.
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Affiliation(s)
- Haoran Chu
- School of Mental Health, Jining Medical University, Jining Shandong 272067.
| | - Cuicui Cui
- Sixth Department of Psychiatry, Shandong Mental Health Center, Jinan 250014, China
| | - Xianbiao Su
- Sixth Department of Psychiatry, Shandong Mental Health Center, Jinan 250014, China
| | - Hongchang Zhang
- Sixth Department of Psychiatry, Shandong Mental Health Center, Jinan 250014, China
| | - Jiashu Ma
- School of Mental Health, Jining Medical University, Jining Shandong 272067
| | - Houming Zhu
- School of Mental Health, Jining Medical University, Jining Shandong 272067
| | - Ludong Bai
- Sixth Department of Psychiatry, Shandong Mental Health Center, Jinan 250014, China
| | - Ranran Li
- Sixth Department of Psychiatry, Shandong Mental Health Center, Jinan 250014, China.
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Nguyen THM, Tinz-Burdick A, Lenhardt M, Geertz M, Ramirez F, Schwartz M, Toledano M, Bonney B, Gaebler B, Liu W, Wolters JF, Chiu K, Fiumera AC, Fiumera HL. Mapping mitonuclear epistasis using a novel recombinant yeast population. PLoS Genet 2023; 19:e1010401. [PMID: 36989278 PMCID: PMC10085025 DOI: 10.1371/journal.pgen.1010401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 04/10/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic variation in mitochondrial and nuclear genomes can perturb mitonuclear interactions and lead to phenotypic differences between individuals and populations. Despite their importance to most complex traits, it has been difficult to identify the interacting mitonuclear loci. Here, we present a novel advanced intercrossed population of Saccharomyces cerevisiae yeasts, called the Mitonuclear Recombinant Collection (MNRC), designed explicitly for detecting mitonuclear loci contributing to complex traits. For validation, we focused on mapping genes that contribute to the spontaneous loss of mitochondrial DNA (mtDNA) that leads to the petite phenotype in yeast. We found that rates of petite formation in natural populations are variable and influenced by genetic variation in nuclear DNA, mtDNA and mitonuclear interactions. We mapped nuclear and mitonuclear alleles contributing to mtDNA stability using the MNRC by integrating a term for mitonuclear epistasis into a genome-wide association model. We found that the associated mitonuclear loci play roles in mitotic growth most likely responding to retrograde signals from mitochondria, while the associated nuclear loci with main effects are involved in genome replication. We observed a positive correlation between growth rates and petite frequencies, suggesting a fitness tradeoff between mitotic growth and mtDNA stability. We also found that mtDNA stability was correlated with a mobile mitochondrial GC-cluster that is present in certain populations of yeast and that selection for nuclear alleles that stabilize mtDNA may be rapidly occurring. The MNRC provides a powerful tool for identifying mitonuclear interacting loci that will help us to better understand genotype-phenotype relationships and coevolutionary trajectories.
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Affiliation(s)
- Tuc H M Nguyen
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
- Department of Biological Sciences, New York University, New York, New York, United States of America
| | - Austen Tinz-Burdick
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Meghan Lenhardt
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Margaret Geertz
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Franchesca Ramirez
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Mark Schwartz
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Michael Toledano
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Brooke Bonney
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Benjamin Gaebler
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Weiwei Liu
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - John F Wolters
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Kenneth Chiu
- Department of Computer Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Anthony C Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, New York, United States of America
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Abstract
PURPOSE OF REVIEW Due to bipolar disorder clinical heterogeneity, a plethora of studies have provided new genetic, epigenetic, molecular, and cellular findings associated with its pathophysiology. RECENT FINDINGS Genome-wide association studies and epigenetic evidence points to genotype-phenotype interactions associated with inflammation, oxidative stress, abnormalities in signaling pathways, hypothalamic-pituitary-adrenal axis, and circadian rhythm linked to mitochondrial dysfunction in bipolar disorder. Although the literature is constantly increasing, most of the genetic variants proposed as biomarkers remain to be validated by independent groups and use bigger samples and longitudinal approaches to enhance their power and predictive ability. SUMMARY Regardless of which of the mechanisms described here plays a primary or secondary role in the pathophysiology of bipolar disorder, all of these interact to worsen clinical outcomes for patients. Identifying new biomarkers for early detection, prognosis, and response to treatment might provide novel targets to prevent progression and promote general well being.
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Kyrgiafini MA, Giannoulis T, Moutou KA, Mamuris Z. Investigating the Impact of a Curse: Diseases, Population Isolation, Evolution and the Mother's Curse. Genes (Basel) 2022; 13:2151. [PMID: 36421825 PMCID: PMC9690142 DOI: 10.3390/genes13112151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 09/08/2024] Open
Abstract
The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the Mother's Curse phenomenon. As mtDNA is inherited from females to all offspring, mutations that are harmful to males tend to accumulate more easily. The Mother's Curse is associated with various diseases, and has a significant effect on males, in many cases even affecting their reproductive ability. Sometimes, it even leads to reproductive isolation, as in crosses between different populations, the mitochondrial genome cannot cooperate effectively with the nuclear one resulting in a mito-nuclear incompatibility and reduce the fitness of the hybrids. This phenomenon is observed both in the laboratory and in natural populations, and have the potential to influence their evolution and speciation. Therefore, it turns out that the study of mitochondria is an exciting field that finds many applications, including pest control, and it can shed light on the molecular mechanism of several diseases, improving successful diagnosis and therapeutics. Finally, mito-nuclear co-adaptation, paternal leakage, and kin selection are some mechanisms that can mitigate the impact of the Mother's Curse.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Katerina A. Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
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Versluys TMM, Flintham EO, Mas-Sandoval A, Savolainen V. Why do we pick similar mates, or do we? Biol Lett 2021; 17:20210463. [PMID: 34813721 DOI: 10.1098/rsbl.2021.0463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Humans often mate with those resembling themselves, a phenomenon described as positive assortative mating (PAM). The causes of this attract broad interest, but there is little agreement on the topic. This may be because empirical studies and reviews sometimes focus on just a few explanations, often based on disciplinary conventions. This review presents an interdisciplinary conceptual framework on the causes of PAM in humans, drawing on human and non-human biology, the social sciences, and the humanities. Viewing causality holistically, we first discuss the proximate causes (i.e. the 'how') of PAM, considering three mechanisms: stratification, convergence and mate choice. We also outline methods to control for confounders when studying mate choice. We then discuss ultimate explanations (i.e. 'the why') for PAM, including adaptive and non-adaptive processes. We conclude by suggesting a focus on interdisciplinarity in future research.
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Affiliation(s)
- Thomas M M Versluys
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Ewan O Flintham
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Alex Mas-Sandoval
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
| | - Vincent Savolainen
- Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, United Kingdom
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