1
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Toyota K. Crustacean endocrinology: Sexual differentiation and potential application for aquaculture. Gen Comp Endocrinol 2024; 356:114578. [PMID: 38971237 DOI: 10.1016/j.ygcen.2024.114578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/08/2024]
Abstract
Crustaceans, which represent a significant subset of arthropods, are classified into three major classes: Ostracoda, Malacostraca, and Branchiopoda. Among them, sex manipulation in decapod species from the Malacostraca class has been extensively researched for aquaculture purposes and to study reproductive physiology and sexual plasticity. Some decapods exhibit sexual dimorphism that influences their biological and economic value. Monosex culture, in which only one sex is cultivated, increases production yields while reducing the risk of invasiveness, as genetic leakage into natural waters is less likely to occur. Differences in yield are also observed when cultivating different sexes, with all-male cultures of Macrobrachium rosenbergii being more profitable than both mixed and all-female cultures. Research on decapod sexual differentiation has led to a better understanding of sex determination and sexual differentiation processes in arthropods. Similar to most mammals and other vertebrate classes, Malacostraca crustaceans, including decapods, exhibit a cell-non-autonomous mode of sexual development. Genetic factors (e.g., sex chromosomes) and endocrine factors (e.g., insulin-like androgenic gland factor and crustacean female sex hormone) play pivotal roles in the development of sexually dimorphic traits. This review synthesizes the existing understanding of sex determination mechanisms and the role of sex hormones in decapod species. Additionally, it provides an overview of the methyl farnesoate, which has been suggested to be involved in male sex differentiation in some crab species, as well as the phenomenon of male-to-female sex reversal in host decapods caused by parasitic crustaceans.
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Affiliation(s)
- Kenji Toyota
- Department of Bioresource Science, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima, Hiroshima 739-8528, Japan; Department of Biological Sciences, Faculty of Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan; Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
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2
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Low GW, Pavlova A, Gan HM, Ko MC, Sadanandan KR, Lee YP, Amos JN, Austin L, Falk S, Dowling DK, Sunnucks P. Accelerated differentiation of neo-W nuclear-encoded mitochondrial genes between two climate-associated bird lineages signals potential co-evolution with mitogenomes. Heredity (Edinb) 2024:10.1038/s41437-024-00718-w. [PMID: 39174672 DOI: 10.1038/s41437-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.
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Affiliation(s)
- Gabriel Weijie Low
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany.
- National Parks Board, 1 Cluny Road, Singapore Botanical Gardens, Singapore, 259569, Singapore.
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- Patriot Biotech Sdn Bhd, 47500, Subang Jaya, Selangor, Malaysia
| | - Meng-Ching Ko
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Keren R Sadanandan
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Yin Peng Lee
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220, Australia
| | - J Nevil Amos
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Arthur Rylah Institute for Environmental Research, Heidelberg, VIC 3084, Australia
| | - Lana Austin
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Stephanie Falk
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
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3
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Laine AL, Tylianakis JM. The coevolutionary consequences of biodiversity change. Trends Ecol Evol 2024; 39:745-756. [PMID: 38705768 DOI: 10.1016/j.tree.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/07/2024]
Abstract
Coevolutionary selection is a powerful process shaping species interactions and biodiversity. Anthropogenic global environmental change is reshaping planetary biodiversity, including by altering the structure and intensity of interspecific interactions. However, remarkably little is understood of how coevolutionary selection is changing in the process. Here, we outline three interrelated pathways - change in evolutionary potential, change in community composition, and shifts in interaction trait distributions - that are expected to redirect coevolutionary selection under biodiversity change. Assessing how both ecological and evolutionary rules governing species interactions are disrupted under anthropogenic global change is of paramount importance to understand the past, present, and future of Earth's biodiversity.
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Affiliation(s)
- Anna-Liisa Laine
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikinkaari 1 (PO Box 65), University of Helsinki, FI-00014 Helsinki, Finland.
| | - Jason M Tylianakis
- Bioprotection Aotearoa, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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4
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Nosek V, Míšek J. Sulfinamide Crossover Reaction. J Org Chem 2024; 89:7927-7932. [PMID: 38785122 PMCID: PMC11165587 DOI: 10.1021/acs.joc.4c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
This study unveils a new catalytic crossover reaction of sulfinamides. Leveraging mild acid catalysis, the reaction demonstrates a high tolerance to structural variations, yielding equimolar products across diverse sulfinamide substrates. Notably, small sulfinamide libraries can be selectively oxidized to sulfonamides, providing a new platform for ligand optimization and discovery in medicinal chemistry. This crossover chemotype provides a new tool for high-throughput experimentation in discovery chemistry.
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Affiliation(s)
- Vladimír Nosek
- Department of Organic Chemistry, Faculty
of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
| | - Jiří Míšek
- Department of Organic Chemistry, Faculty
of Science, Charles University in Prague, Hlavova 2030/8, 12843 Prague 2, Czech Republic
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5
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Daigle A, Johri P. Hill-Robertson interference may bias the inference of fitness effects of new mutations in highly selfing species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579142. [PMID: 38370745 PMCID: PMC10871249 DOI: 10.1101/2024.02.06.579142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The accurate estimation of the distribution of fitness effects (DFE) of new mutations is critical for population genetic inference but remains a challenging task. While various methods have been developed for DFE inference using the site frequency spectrum of putatively neutral and selected sites, their applicability in species with diverse life history traits and complex demographic scenarios is not well understood. Selfing is common among eukaryotic species and can lead to decreased effective recombination rates, increasing the effects of selection at linked sites, including interference between selected alleles. We employ forward simulations to investigate the limitations of current DFE estimation approaches in the presence of selfing and other model violations, such as linkage, departures from semidominance, population structure, and uneven sampling. We find that distortions of the site frequency spectrum due to Hill-Robertson interference in highly selfing populations lead to mis-inference of the deleterious DFE of new mutations. Specifically, while accounting for the decrease in the effective population size due to linked effects of selection allows an accurate estimation of selection coefficients in moderately selfing populations, this correction is unable to accurately estimate selection coefficients in highly selfing populations when interference between selected alleles is pervasive. In addition, the presence of cryptic population structure with low rates of migration and uneven sampling across subpopulations leads to the false inference of a deleterious DFE skewed towards effectively neutral/mildly deleterious mutations. Finally, the proportion of adaptive substitutions estimated at high rates of selfing is substantially overestimated. Our observations apply broadly to species and genomic regions with little/no recombination and where interference might be pervasive.
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6
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Sharma DK, Rajpurohit YS. Multitasking functions of bacterial extracellular DNA in biofilms. J Bacteriol 2024; 206:e0000624. [PMID: 38445859 PMCID: PMC11025335 DOI: 10.1128/jb.00006-24] [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] [Indexed: 03/07/2024] Open
Abstract
Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.
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Affiliation(s)
- Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Schools of Life Sciences, Homi Bhabha National Institute (DAE—Deemed University), Mumbai, India
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7
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Wu C, Cheng Z, Gao J. Mysterious Bamboo flowering phenomenon: A literature review and new perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168695. [PMID: 38000754 DOI: 10.1016/j.scitotenv.2023.168695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Bamboo, a globally distributed non-timber forest resource, plays a critical role in local ecosystems and economies. Despite its significance, the understanding of bamboo's long and unpredictable flowering cycles remains limited. Our bibliometric analysis of bamboo flowering-related literature from the Web of Science database reveals an initial focus on regeneration studies, with a recent trend shifting towards microscopic and molecular perspectives. Furthermore, our narrative review emphasizes the importance of considering factors such as the proportion of flowering culms and the duration of flowering in classifying bamboo flowering phenomena. While numerous studies have endorsed the predator saturation hypothesis as a suitable explanation for the synchronicity of bamboo flowering, no existing theory explains bamboo's prolonged flowering cycles. We propose a new natural selection hypothesis as a potential explanation for these extraordinary cycles, underscoring the need for further research in this area. Despite the substantial volume of data accumulated on bamboo flowering, these resources have not been fully exploited in recent research. Future studies would benefit from more comprehensive data collection methods, encompassing field observations, satellite remote sensing data, and omics data. The convergence of traditional ecological studies with molecular techniques may pave the way for significant advancements in bamboo flowering research.
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Affiliation(s)
- Chongyang Wu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China
| | - Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology/International Center for Bamboo and Rattan, Beijing, PR China.
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8
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Chase MA, Vilcot M, Mugal CF. The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome †. Proc Biol Sci 2024; 291:20232382. [PMID: 38228173 DOI: 10.1098/rspb.2023.2382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Recombination is a central evolutionary process that reshuffles combinations of alleles along chromosomes, and consequently is expected to influence the efficacy of direct selection via Hill-Robertson interference. Additionally, the indirect effects of selection on neutral genetic diversity are expected to show a negative relationship with recombination rate, as background selection and genetic hitchhiking are stronger when recombination rate is low. However, owing to the limited availability of recombination rate estimates across divergent species, the impact of evolutionary changes in recombination rate on genomic signatures of selection remains largely unexplored. To address this question, we estimate recombination rate in two Ficedula flycatcher species, the taiga flycatcher (Ficedula albicilla) and collared flycatcher (Ficedula albicollis). We show that recombination rate is strongly correlated with signatures of indirect selection, and that evolutionary changes in recombination rate between species have observable impacts on this relationship. Conversely, signatures of direct selection on coding sequences show little to no relationship with recombination rate, even when restricted to genes where recombination rate is conserved between species. Thus, using measures of indirect and direct selection that bridge micro- and macro-evolutionary timescales, we demonstrate that the role of recombination rate and its dynamics varies for different signatures of selection.
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Affiliation(s)
- Madeline A Chase
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
- Swiss Ornithological Institute, 6204 Sempach, Switzerland
| | - Maurine Vilcot
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
- CEFE, University of Montpellier, CNRS, EPHE, IRD, 34293 Montpellier 5, France
| | - Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
- Laboratory of Biometry and Evolutionary Biology, University of Lyon 1, CNRS UMR 5558, 69622 Villeurbanne cedex, France
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9
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Filatov DA. Evolution of a plant sex chromosome driven by expanding pericentromeric recombination suppression. Sci Rep 2024; 14:1373. [PMID: 38228625 DOI: 10.1038/s41598-024-51153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/01/2024] [Indexed: 01/18/2024] Open
Abstract
Recombination suppression around sex-determining gene(s) is a key step in evolution of sex chromosomes, but it is not well understood how it evolves. Recently evolved sex-linked regions offer an opportunity to understand the mechanisms of recombination cessation. This paper analyses such a region on Silene latifolia (Caryophyllaceae) sex chromosomes, where recombination was suppressed in the last 120 thousand years ("stratum 3"). Locating the boundaries of the stratum 3 in S. latifolia genome sequence revealed that this region is far larger than assumed previously-it is about 14 Mb long and includes 202 annotated genes. A gradient of X:Y divergence detected in the stratum 3, with divergence increasing proximally, indicates gradual recombination cessation, possibly caused by expansion of pericentromeric recombination suppression (PRS) into the pseudoautosomal region. Expansion of PRS was also the likely cause for the formation of the older stratum 2 on S. latifolia sex chromosomes. The role of PRS in sex chromosome evolution has been underappreciated, but it may be a significant factor, especially in the species with large chromosomes where PRS is often extensive.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
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10
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Miller SM, Stuart KC, Burke NW, Rollins LA, Bonduriansky R. Genetic and Phenotypic Consequences of Local Transitions between Sexual and Parthenogenetic Reproduction in the Wild. Am Nat 2024; 203:73-91. [PMID: 38207137 DOI: 10.1086/727511] [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] [Indexed: 01/13/2024]
Abstract
AbstractTransitions from sexual to asexual reproduction have occurred in numerous lineages, but it remains unclear why asexual populations rarely persist. In facultatively parthenogenetic animals, all-female populations can arise when males are absent or become extinct, and such populations could help to understand the genetic and phenotypic changes that occur in the initial stages of transitions to asexuality. We investigated a naturally occurring spatial mosaic of mixed-sex and all-female populations of the facultatively parthenogenetic Australian phasmid Megacrania batesii. Analysis of single-nucleotide polymorphisms indicated multiple independent transitions between reproductive modes. All-female populations had much lower heterozygosity and allelic diversity than mixed-sex populations, but we found few consistent differences in fitness-related traits between population types. All-female populations exhibited more frequent and severe deformities in their (flight-incapable) wings but did not show higher rates of appendage loss. All-female populations also harbored more ectoparasites in swamp (but not beach) habitats. Reproductive mode explained little variation in female body size, fecundity, or egg hatch rate. Our results suggest that transitions to parthenogenetic reproduction can lead to dramatic genetic changes with little immediate effect on performance. All-female M. batesii populations appear to consist of high-fitness genotypes that might be able to thrive for many generations in relatively constant and benign environments but could be vulnerable to environmental challenges, such as increased parasite abundance.
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11
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Rödelsperger C. Comparative Genomics of Sex, Chromosomes, and Sex Chromosomes in Caenorhabditis elegans and Other Nematodes. Methods Mol Biol 2024; 2802:455-472. [PMID: 38819568 DOI: 10.1007/978-1-0716-3838-5_15] [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] [Indexed: 06/01/2024]
Abstract
The nematode phylum has evolved a remarkable diversity of reproductive modes, including the repeated emergence of asexuality and hermaphroditism across divergent clades. The species-richness and small genome size of nematodes make them ideal systems for investigating the genome-wide causes and consequences of such major transitions. The availability of functional annotations for most Caenorhabditis elegans genes further allows the linking of patterns of gene content evolution with biological processes. Such gene-centric studies were recently complemented by investigations of chromosome evolution that made use of the first chromosome-scale genome assemblies outside the Caenorhabditis genus. This review highlights recent comparative genomic studies of reproductive mode evolution addressing the hybrid origin of asexuality and the parallel gene loss following the emergence of hermaphroditism. It further summarizes ongoing efforts to characterize ancient linkage blocks called Nigon elements, which form central units of chromosome evolution. Fusions between Nigon elements have been demonstrated to impact recombination and speciation. Finally, multiple recent fusions between autosomal and the sex-linked Nigon element reveal insights into the dynamic evolution of sex chromosomes across various timescales.
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Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
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12
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Brekke C, Johnston SE, Knutsen TM, Berg P. Genetic architecture of individual meiotic crossover rate and distribution in Atlantic Salmon. Sci Rep 2023; 13:20481. [PMID: 37993527 PMCID: PMC10665409 DOI: 10.1038/s41598-023-47208-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Meiotic recombination through chromosomal crossovers ensures proper segregation of homologous chromosomes during meiosis, while also breaking down linkage disequilibrium and shuffling alleles at loci located on the same chromosome. Rates of recombination can vary between species, but also between and within individuals, sex and chromosomes within species. Indeed, the Atlantic salmon genome is known to have clear sex differences in recombination with female biased heterochiasmy and markedly different landscapes of crossovers between males and females. In male meiosis, crossovers occur strictly in the telomeric regions, whereas in female meiosis crossovers tend to occur closer to the centromeres. However, little is known about the genetic control of these patterns and how this differs at the individual level. Here, we investigate genetic variation in individual measures of recombination in > 5000 large full-sib families of a Norwegian Atlantic salmon breeding population with high-density SNP genotypes. We show that females had 1.6 × higher crossover counts (CC) than males, with autosomal linkage maps spanning a total of 2174 cM in females and 1483 cM in males. However, because of the extreme telomeric bias of male crossovers, female recombination is much more important for generation of new haplotypes with 8 × higher intra-chromosomal genetic shuffling than males. CC was heritable in females (h2 = 0.11) and males (h2 = 0.10), and shuffling was also heritable in both sex but with a lower heritability in females (h2 = 0.06) than in males (h2 = 0.11). Inter-sex genetic correlations for both traits were close to zero, suggesting that rates and distribution of crossovers are genetically distinct traits in males and females, and that there is a potential for independent genetic change in both sexes in the Atlantic Salmon. Together, these findings give novel insights into the genetic architecture of recombination in salmonids and contribute to a better understanding of how rates and distribution of recombination may evolve in eukaryotes more broadly.
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Affiliation(s)
- Cathrine Brekke
- Institute of Ecology and Evolution, School of Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Post Box 5003, 1433, Ås, Norway.
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | | | - Peer Berg
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Post Box 5003, 1433, Ås, Norway
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13
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Dluzewska J, Dziegielewski W, Szymanska-Lejman M, Gazecka M, Henderson IR, Higgins JD, Ziolkowski PA. MSH2 stimulates interfering and inhibits non-interfering crossovers in response to genetic polymorphism. Nat Commun 2023; 14:6716. [PMID: 37872134 PMCID: PMC10593791 DOI: 10.1038/s41467-023-42511-z] [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: 04/17/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Meiotic crossovers can be formed through the interfering pathway, in which one crossover prevents another from forming nearby, or by an independent non-interfering pathway. In Arabidopsis, local sequence polymorphism between homologs can stimulate interfering crossovers in a MSH2-dependent manner. To understand how MSH2 regulates crossovers formed by the two pathways, we combined Arabidopsis mutants that elevate non-interfering crossovers with msh2 mutants. We demonstrate that MSH2 blocks non-interfering crossovers at polymorphic loci, which is the opposite effect to interfering crossovers. We also observe MSH2-independent crossover inhibition at highly polymorphic sites. We measure recombination along the chromosome arms in lines differing in patterns of heterozygosity and observe a MSH2-dependent crossover increase at the boundaries between heterozygous and homozygous regions. Here, we show that MSH2 is a master regulator of meiotic DSB repair in Arabidopsis, with antagonistic effects on interfering and non-interfering crossovers, which shapes the crossover landscape in relation to interhomolog polymorphism.
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Affiliation(s)
- Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Monika Gazecka
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
- Department of Molecular Virology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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14
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Rimbault M, Legeai F, Peccoud J, Mieuzet L, Call E, Nouhaud P, Defendini H, Mahéo F, Marande W, Théron N, Tagu D, Le Trionnaire G, Simon JC, Jaquiéry J. Contrasting Evolutionary Patterns Between Sexual and Asexual Lineages in a Genomic Region Linked to Reproductive Mode Variation in the pea aphid. Genome Biol Evol 2023; 15:evad168. [PMID: 37717171 PMCID: PMC10538257 DOI: 10.1093/gbe/evad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Although asexual lineages evolved from sexual lineages in many different taxa, the genetics of sex loss remains poorly understood. We addressed this issue in the pea aphid Acyrthosiphon pisum, whose natural populations encompass lineages performing cyclical parthenogenesis (CP) and producing one sexual generation per year, as well as obligate parthenogenetic (OP) lineages that can no longer produce sexual females but can still produce males. An SNP-based, whole-genome scan of CP and OP populations sequenced in pools (103 individuals from 6 populations) revealed that an X-linked region is associated with the variation in reproductive mode. This 840-kb region is highly divergent between CP and OP populations (FST = 34.9%), with >2,000 SNPs or short Indels showing a high degree of association with the phenotypic trait. In OP populations specifically, this region also shows reduced diversity and Tajima's D, consistent with the OP phenotype being a derived trait in aphids. Interestingly, the low genetic differentiation between CP and OP populations at the rest of the genome (FST = 2.5%) suggests gene flow between them. Males from OP lineages thus likely transmit their op allele to new genomic backgrounds. These genetic exchanges, combined with the selection of the OP and CP reproductive modes under different climates, probably contribute to the long-term persistence of the cp and op alleles.
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Affiliation(s)
- Maud Rimbault
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Fabrice Legeai
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- University of Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, Poitiers CEDEX 9, France
| | - Lucie Mieuzet
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Elsa Call
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Pierre Nouhaud
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Hélène Defendini
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Frédérique Mahéo
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - William Marande
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Nicolas Théron
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Denis Tagu
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Gaël Le Trionnaire
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Jean-Christophe Simon
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Julie Jaquiéry
- INRAE, UMR 1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
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15
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Travers-Cook TJ, Jokela J, Buser CC. The evolutionary ecology of fungal killer phenotypes. Proc Biol Sci 2023; 290:20231108. [PMID: 37583325 PMCID: PMC10427833 DOI: 10.1098/rspb.2023.1108] [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: 05/17/2023] [Accepted: 07/20/2023] [Indexed: 08/17/2023] Open
Abstract
Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.
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Affiliation(s)
- Thomas J. Travers-Cook
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Jukka Jokela
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Claudia C. Buser
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
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16
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Tsui V, Lyu R, Novakovic S, Stringer JM, Dunleavy JE, Granger E, Semple T, Leichter A, Martelotto LG, Merriner DJ, Liu R, McNeill L, Zerafa N, Hoffmann ER, O’Bryan MK, Hutt K, Deans AJ, Heierhorst J, McCarthy DJ, Crismani W. Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals. CELL GENOMICS 2023; 3:100349. [PMID: 37601968 PMCID: PMC10435384 DOI: 10.1016/j.xgen.2023.100349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/30/2023] [Accepted: 06/02/2023] [Indexed: 08/22/2023]
Abstract
Meiotic crossovers are required for accurate chromosome segregation and producing new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. Here, we reveal the tumor suppressor FANCM as a meiotic anti-crossover factor in mammals. We use unique large-scale crossover analyses with both single-gamete sequencing and pedigree-based bulk-sequencing datasets to identify a genome-wide increase in crossover frequencies in Fancm-deficient mice. Gametogenesis is heavily perturbed in Fancm loss-of-function mice, which is consistent with the reproductive defects reported in humans with biallelic FANCM mutations. A portion of the gametogenesis defects can be attributed to the cGAS-STING pathway after birth. Despite the gametogenesis phenotypes in Fancm mutants, both sexes are capable of producing offspring. We propose that the anti-crossover function and role in gametogenesis of Fancm are separable and will inform diagnostic pathways for human genomic instability disorders.
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Affiliation(s)
- Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Stevan Novakovic
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jessica M. Stringer
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Jessica E.M. Dunleavy
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Elissah Granger
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Tim Semple
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Anna Leichter
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Luciano G. Martelotto
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - D. Jo Merriner
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruijie Liu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Lucy McNeill
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Nadeen Zerafa
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Eva R. Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Moira K. O’Bryan
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Deans
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Genome Stability Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jörg Heierhorst
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Molecular Genetics Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
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17
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Li C, Tao L, Guan G, Guan Z, Perry AM, Hu T, Bing J, Xu M, Nobile CJ, Huang G. Atmospheric humidity regulates same-sex mating in Candida albicans through the trehalose and osmotic signaling pathways. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1915-1929. [PMID: 37118508 PMCID: PMC10631464 DOI: 10.1007/s11427-023-2309-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/01/2023] [Indexed: 04/30/2023]
Abstract
Sexual reproduction is prevalent in eukaryotic organisms and plays a critical role in the evolution of new traits and in the generation of genetic diversity. Environmental factors often have a direct impact on the occurrence and frequency of sexual reproduction in fungi. The regulatory effects of atmospheric relative humidity (RH) on sexual reproduction and pathogenesis in plant fungal pathogens and in soil fungi have been extensively investigated. However, the knowledge of how RH regulates the lifecycles of human fungal pathogens is limited. In this study, we report that low atmospheric RH promotes the development of mating projections and same-sex (homothallic) mating in the human fungal pathogen Candida albicans. Low RH causes water loss in C. albicans cells, which results in osmotic stress and the generation of intracellular reactive oxygen species (ROS) and trehalose. The water transporting aquaporin Aqy1, and the G-protein coupled receptor Gpr1 function as cell surface sensors of changes in atmospheric humidity. Perturbation of the trehalose metabolic pathway by inactivating trehalose synthase or trehalase promotes same-sex mating in C. albicans by increasing osmotic or ROS stresses, respectively. Intracellular trehalose and ROS signal the Hog1-osmotic and Hsf1-Hsp90 signaling pathways to regulate the mating response. We, therefore, propose that the cell surface sensors Aqy1 and Gpr1, intracellular trehalose and ROS, and the Hog1-osmotic and Hsf1-Hsp90 signaling pathways function coordinately to regulate sexual mating in response to low atmospheric RH conditions in C. albicans.
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Affiliation(s)
- Chao Li
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Tao
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Guobo Guan
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhangyue Guan
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Austin M Perry
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, 95343, USA
| | - Tianren Hu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jian Bing
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ming Xu
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, University of California, Merced, Merced, CA, 95343, USA
- Health Sciences Research Institute, University of California, Merced, Merced, CA, 95343, USA
| | - Guanghua Huang
- Department of Infectious Diseases, Huashan Hospital, Shanghai Institute of Infectious Disease and Biosecurity and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, 200052, China.
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18
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Haider M, Schilling MP, Moest MH, Steiner FM, Schlick‐Steiner BC, Arthofer W. Evolutionary history of an Alpine Archaeognath ( Machilis pallida): Insights from different variant. Ecol Evol 2023; 13:e10227. [PMID: 37404697 PMCID: PMC10316371 DOI: 10.1002/ece3.10227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/06/2023] Open
Abstract
Reconstruction of species histories is a central aspect of evolutionary biology. Patterns of genetic variation within and among populations can be leveraged to elucidate evolutionary processes and demographic histories. However, interpreting genetic signatures and unraveling the contributing processes can be challenging, in particular for non-model organisms with complex reproductive modes and genome organization. One way forward is the combined consideration of patterns revealed by different molecular markers (nuclear vs. mitochondrial) and types of variants (common vs. rare) that differ in their age, mode, and rate of evolution. Here, we applied this approach to RNAseq data generated for Machilis pallida (Archaeognatha), an Alpine jumping bristletail considered parthenogenetic and triploid. We generated de novo transcriptome and mitochondrial assemblies to obtain high-density data to investigate patterns of mitochondrial and common and rare nuclear variation in 17 M. pallida individuals sampled from all known populations. We find that the different variant types capture distinct aspects of the evolutionary history and discuss the observed patterns in the context of parthenogenesis, polyploidy, and survival during glaciation. This study highlights the potential of different variant types to gain insights into evolutionary scenarios even from challenging but often available data and the suitability of M. pallida and the genus Machilis as a study system for the evolution of sexual strategies and polyploidization during environmental change. We also emphasize the need for further research which will be stimulated and facilitated by these newly generated resources and insights.
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Affiliation(s)
- Marlene Haider
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | - Martin P. Schilling
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | - Markus H. Moest
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | - Florian M. Steiner
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
| | | | - Wolfgang Arthofer
- Department of Ecology, Molecular Ecology GroupUniversity of InnsbruckInnsbruckAustria
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19
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Valero-Regalón FJ, Solé M, López-Jiménez P, Valerio-de Arana M, Martín-Ruiz M, de la Fuente R, Marín-Gual L, Renfree MB, Shaw G, Berríos S, Fernández-Donoso R, Waters PD, Ruiz-Herrera A, Gómez R, Page J. Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials. Front Cell Dev Biol 2023; 11:1147610. [PMID: 37181752 PMCID: PMC10166821 DOI: 10.3389/fcell.2023.1147610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
In eutherian mammals, hundreds of programmed DNA double-strand breaks (DSBs) are generated at the onset of meiosis. The DNA damage response is then triggered. Although the dynamics of this response is well studied in eutherian mammals, recent findings have revealed different patterns of DNA damage signaling and repair in marsupial mammals. To better characterize these differences, here we analyzed synapsis and the chromosomal distribution of meiotic DSBs markers in three different marsupial species (Thylamys elegans, Dromiciops gliorides, and Macropus eugenii) that represent South American and Australian Orders. Our results revealed inter-specific differences in the chromosomal distribution of DNA damage and repair proteins, which were associated with differing synapsis patterns. In the American species T. elegans and D. gliroides, chromosomal ends were conspicuously polarized in a bouquet configuration and synapsis progressed exclusively from the telomeres towards interstitial regions. This was accompanied by sparse H2AX phosphorylation, mainly accumulating at chromosomal ends. Accordingly, RAD51 and RPA were mainly localized at chromosomal ends throughout prophase I in both American marsupials, likely resulting in reduced recombination rates at interstitial positions. In sharp contrast, synapsis initiated at both interstitial and distal chromosomal regions in the Australian representative M. eugenii, the bouquet polarization was incomplete and ephemeral, γH2AX had a broad nuclear distribution, and RAD51 and RPA foci displayed an even chromosomal distribution. Given the basal evolutionary position of T. elegans, it is likely that the meiotic features reported in this species represent an ancestral pattern in marsupials and that a shift in the meiotic program occurred after the split of D. gliroides and the Australian marsupial clade. Our results open intriguing questions about the regulation and homeostasis of meiotic DSBs in marsupials. The low recombination rates observed at the interstitial chromosomal regions in American marsupials can result in the formation of large linkage groups, thus having an impact in the evolution of their genomes.
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Affiliation(s)
| | - Mireia Solé
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular, Universitat Autònoma de Barcelona, Spain
| | - Pablo López-Jiménez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Valerio-de Arana
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Roberto de la Fuente
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of The Polish Academy of Sciences, Jastrzębiec, Poland
| | - Laia Marín-Gual
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Soledad Berríos
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Raúl Fernández-Donoso
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Rocío Gómez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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20
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Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Mol Ecol 2023; 32:1441-1457. [PMID: 36433653 PMCID: PMC10946714 DOI: 10.1111/mec.16793] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
The term "haplotype block" is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a "hard" selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Arka Pal
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Sean Stankowski
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Nicholas H Barton
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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21
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Ziolkowski PA. Why do plants need the ZMM crossover pathway? A snapshot of meiotic recombination from the perspective of interhomolog polymorphism. PLANT REPRODUCTION 2023; 36:43-54. [PMID: 35819509 PMCID: PMC9958190 DOI: 10.1007/s00497-022-00446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 06/06/2023]
Abstract
At the heart of meiosis is crossover recombination, i.e., reciprocal exchange of chromosome fragments between parental genomes. Surprisingly, in most eukaryotes, including plants, several recombination pathways that can result in crossover event operate in parallel during meiosis. These pathways emerged independently in the course of evolution and perform separate functions, which directly translate into their roles in meiosis. The formation of one crossover per chromosome pair is required for proper chromosome segregation. This "obligate" crossover is ensured by the major crossover pathway in plants, and in many other eukaryotes, known as the ZMM pathway. The secondary pathways play important roles also in somatic cells and function mainly as repair mechanisms for DNA double-strand breaks (DSBs) not used for crossover formation. One of the consequences of the functional differences between ZMM and other DSB repair pathways is their distinct sensitivities to polymorphisms between homologous chromosomes. From a population genetics perspective, these differences may affect the maintenance of genetic variability. This might be of special importance when considering that a significant portion of plants uses inbreeding as a predominant reproductive strategy, which results in loss of interhomolog polymorphism. While we are still far from fully understanding the relationship between meiotic recombination pathways and genetic variation in populations, recent studies of crossovers in plants offer a new perspective.
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Affiliation(s)
- Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland.
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22
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Heterochiasmy and Sex Chromosome Evolution in Silene. Genes (Basel) 2023; 14:genes14030543. [PMID: 36980816 PMCID: PMC10048291 DOI: 10.3390/genes14030543] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
The evolution of a non-recombining sex-specific region is a key step in sex chromosome evolution. Suppression of recombination between the (proto-) X- and Y-chromosomes in male meiosis creates a non-recombining Y-linked region (NRY), while the X-chromosome continues to recombine in females. Lack of recombination in the NRY defines its main properties—genetic degeneration and accumulation of repetitive DNA, making X and Y chromosomes very different from each other. How and why recombination suppression on sex chromosomes evolves remains controversial. A strong difference in recombination rates between the sexes (heterochiasmy) can facilitate or even cause recombination suppression. In the extreme case—complete lack of recombination in the heterogametic sex (achiasmy)—the entire sex-specific chromosome is automatically non-recombining. In this study, I analyse sex-specific recombination rates in a dioecious plant Silene latifolia (Caryophyllaceae), which evolved separate sexes and sex chromosomes ~11 million years ago. I reconstruct high-density RNAseq-based genetic maps including over five thousand genic markers for the two sexes separately. The comparison of the male and female maps reveals only modest heterochiasmy across the genome, with the exception of the sex chromosomes, where recombination is suppressed in males. This indicates that heterochiasmy likely played only a minor, if any, role in NRY evolution in S. latifolia, as recombination suppression is specific to NRY rather than to the entire genome in males. Other mechanisms such as structural rearrangements and/or epigenetic modifications were likely involved, and comparative genome analysis and genetic mapping in multiple Silene species will help to shed light on the mechanism(s) of recombination suppression that led to the evolution of sex chromosomes.
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23
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Brekke C, Johnston SE, Gjuvsland AB, Berg P. Variation and genetic control of individual recombination rates in Norwegian Red dairy cattle. J Dairy Sci 2023; 106:1130-1141. [PMID: 36543643 DOI: 10.3168/jds.2022-22368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/06/2022] [Indexed: 12/24/2022]
Abstract
Meiotic recombination is an important evolutionary mechanism that breaks up linkages between loci and creates novel haplotypes for selection to act upon. Understanding the genetic control of variation in recombination rates is therefore of great interest in both natural and domestic breeding populations. In this study, we used pedigree information and medium-density (∼50K) genotyped data in a large cattle (Bos taurus) breeding population in Norway (Norwegian Red cattle) to investigate recombination rate variation between sexes and individual animals. Sex-specific linkage mapping showed higher rates in males than in females (total genetic length of autosomes = 2,492.9 cM in males and 2,308.9 cM in females). However, distribution of recombination along the genome showed little variation between males and females compared with that in other species. The heritability of autosomal crossover count was low but significant in both sexes (h2 = 0.04 and 0.09 in males and females, respectively). We identified 2 loci associated with variation in individual crossover counts in female, one close to the candidate gene CEP55 and one close to both MLH3 and NEK9. All 3 genes have been associated with recombination rates in other cattle breeds. Our study contributes to the understanding of how recombination rates are controlled and how they may vary between closely related breeds as well as between species.
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Affiliation(s)
- C Brekke
- Norwegian University of Life Sciences, Department of Animal and Aquacultural sciences, Oluf Thesens vei 6, 1433 Ås, Norway.
| | - S E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | | | - P Berg
- Norwegian University of Life Sciences, Department of Animal and Aquacultural sciences, Oluf Thesens vei 6, 1433 Ås, Norway
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24
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Huang Q, Sim SB, Geib SM, Childers A, Liu J, Wei X, Han W, Posada-Florez F, Xue AZ, Li Z, Evans JD. Identification of sex chromosomes and primary sex ratio in the small hive beetle, a worldwide parasite of honey bees. Gigascience 2022; 12:giad056. [PMID: 37489752 PMCID: PMC10367126 DOI: 10.1093/gigascience/giad056] [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: 02/08/2023] [Revised: 04/20/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The small hive beetle (SHB), Aethina tumida, has emerged as a worldwide threat to honey bees in the past two decades. These beetles harvest nest resources, feed on larval bees, and ultimately spoil nest resources with gelatinous slime together with the fungal symbiont Kodamaea ohmeri. RESULTS Here, we present the first chromosome-level genome assembly for the SHB. With a 99.1% representation of conserved (BUSCO) arthropod genes, this resource enables the study of chemosensory, digestive, and detoxification traits critical for SHB success and possible control. We use this annotated assembly to characterize features of SHB sex chromosomes and a female-skewed primary sex ratio. We also found chromosome fusion and a lower recombination rate in sex chromosomes than in autosomes. CONCLUSIONS Genome-enabled insights will clarify the traits that allowed this beetle to exploit hive resources successfully and will be critical for determining the causes of observed sex ratio asymmetries.
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Affiliation(s)
- Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sheina B Sim
- Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research, USDA, Agricultural Research Service, Hilo, HI 96720, USA
| | - Scott M Geib
- Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research, USDA, Agricultural Research Service, Hilo, HI 96720, USA
| | - Anna Childers
- Beltsville Agricultural Research Center, Bee Research Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Junfeng Liu
- Periodicals Agency, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Xiuxiu Wei
- Honeybee Research Institute, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Wensu Han
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Francisco Posada-Florez
- Beltsville Agricultural Research Center, Bee Research Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Allen Z Xue
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jay D Evans
- Beltsville Agricultural Research Center, Bee Research Laboratory, USDA, Agricultural Research Service, Beltsville, MD 20705, USA
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Characterization of DNA Processing Protein A (DprA) of the Radiation-Resistant Bacterium Deinococcus radiodurans. Microbiol Spectr 2022; 10:e0347022. [PMID: 36453941 PMCID: PMC9769556 DOI: 10.1128/spectrum.03470-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Environmental DNA uptake by certain bacteria and its integration into their genome create genetic diversity and new phenotypes. DNA processing protein A (DprA) is part of a multiprotein complex and facilitates the natural transformation (NT) phenotype in most bacteria. Deinococcus radiodurans, an extremely radioresistant bacterium, is efficient in NT, and its genome encodes nearly all of the components of the natural competence complex. Here, we have characterized the DprA protein of this bacterium (DrDprA) for the known characteristics of DprA proteins of other bacteria and the mechanisms underlying the DNA-RecA interaction. DrDprA has three domains. In vitro studies showed that purified recombinant DrDprA binds to both single-strand DNA (ssDNA) and double-strand DNA (dsDNA) and is able to protect ssDNA from nucleolytic degradation. DrDprA showed a strong interaction with DrRecA and facilitated RecA-catalyzed functions in vivo. Mutational studies identified DrDprA amino acid residues crucial for oligomerization, the interaction with DrRecA, and DNA binding. Furthermore, we showed that both oligomerization and DNA binding properties of DrDprA are integral to its support of the DrRecA-catalyzed strand exchange reaction (SER) in vitro. Together, these data suggested that DrDprA is largely structurally conserved with other DprA homologs but shows some unique structure-function features like the existence of an additional C-terminal Drosophila melanogaster Miasto-like protein 1 (DML1) domain, equal affinities for ssDNA and dsDNA, and the collective roles of oligomerization and DNA binding properties in supporting DrRecA functions. IMPORTANCE Bacteria can take up extracellular DNA (eDNA) by natural transformation (NT). Many bacteria, including Deinococcus radiodurans, have constitutive competence systems and can take up eDNA throughout their growth phase. DprA (DNA processing protein A) is a transformation-specific recombination mediator protein (RMP) that plays a role in bacterial NT, and the absence of this gene significantly reduces the transformation efficiencies of both chromosomal and plasmid DNA. NT helps bacteria survive under adverse conditions and contributes to genetic diversity in bacteria. The present work describes the characterization of DprA from D. radiodurans and will add to the existing knowledge of DprA biology.
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Tóth A, Székvölgyi L, Vellai T. The genome loading model for the origin and maintenance of sex in eukaryotes. Biol Futur 2022; 73:345-357. [PMID: 36534301 DOI: 10.1007/s42977-022-00148-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Understanding why sexual reproduction-which involves syngamy (union of gametes) and meiosis-emerged and how it has subsisted for millions of years remains a fundamental problem in biology. Considered as the essence of sex, meiotic recombination is initiated by a DNA double-strand break (DSB) that forms on one of the pairing homologous chromosomes. This DNA lesion is subsequently repaired by gene conversion, the non-reciprocal transfer of genetic information from the intact homolog. A major issue is which of the pairing homologs undergoes DSB formation. Accumulating evidence shows that chromosomal sites where the pairing homologs locally differ in size, i.e., are heterozygous for an insertion or deletion, often display disparity in gene conversion. Biased conversion tends to duplicate insertions and lose deletions. This suggests that DSB is preferentially formed on the "shorter" homologous region, which thereby acts as the recipient for DNA transfer. Thus, sex primarily functions as a genome (re)loading mechanism. It ensures the restoration of formerly lost DNA sequences (deletions) and allows the efficient copying and, mainly in eukaryotes, subsequent spreading of newly emerged sequences (insertions) arising initially in an individual genome, even if they confer no advantage to the host. In this way, sex simultaneously repairs deletions and increases genetic variability underlying adaptation. The model explains a remarkable increase in DNA content during the evolution of eukaryotic genomes.
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Affiliation(s)
- András Tóth
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary.
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27
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Ma W, Rovatsos M. Sex chromosome evolution: The remarkable diversity in the evolutionary rates and mechanisms. J Evol Biol 2022; 35:1581-1588. [DOI: 10.1111/jeb.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 12/03/2022]
Affiliation(s)
- Wen‐Juan Ma
- Department of Molecular Biosciences University of Kansas Lawrence Kansas USA
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28
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Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations. PLoS Comput Biol 2022; 18:e1010710. [DOI: 10.1371/journal.pcbi.1010710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/05/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding the benefits and costs of recombination under different scenarios of evolutionary adaptation remains an open problem for theoretical and experimental research. In this study, we focus on finite populations evolving on neutral networks comprising viable and unfit genotypes. We provide a comprehensive overview of the effects of recombination by jointly considering different measures of evolvability and mutational robustness over a broad parameter range, such that many evolutionary regimes are covered. We find that several of these measures vary non-monotonically with the rates of mutation and recombination. Moreover, the presence of unfit genotypes that introduce inhomogeneities in the network of viable states qualitatively alters the effects of recombination. We conclude that conflicting trends induced by recombination can be explained by an emerging trade-off between evolvability on the one hand, and mutational robustness on the other. Finally, we discuss how different implementations of the recombination scheme in theoretical models can affect the observed dependence on recombination rate through a coupling between recombination and genetic drift.
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29
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Winbush A, Singh ND. Variation in fine-scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection. G3 GENES|GENOMES|GENETICS 2022; 12:6663992. [PMID: 35961026 PMCID: PMC9526048 DOI: 10.1093/g3journal/jkac208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022]
Abstract
Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection, but the extent to which fine-scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here, we utilize a set of 3 temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes, including recombination rate, based on the temperature regime in which they evolved. Using whole-genome sequencing data from these populations, we generated linkage disequilibrium-based fine-scale recombination maps for each population. With these maps, we compare recombination rates and patterns among the 3 populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the 3 populations. Lastly, we show variation in localized regions of enhanced recombination rates, termed warm spots, between the populations with these warm spots and associated genes overlapping areas previously shown to have diverged in the 3 populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.
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Affiliation(s)
- Ari Winbush
- Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR 97403, USA
| | - Nadia D Singh
- Department of Biology, Institute of Ecology and Evolution, University of Oregon , Eugene, OR 97403, USA
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30
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Schield DR, Perry BW, Adams RH, Holding ML, Nikolakis ZL, Gopalan SS, Smith CF, Parker JM, Meik JM, DeGiorgio M, Mackessy SP, Castoe TA. The roles of balancing selection and recombination in the evolution of rattlesnake venom. Nat Ecol Evol 2022; 6:1367-1380. [PMID: 35851850 PMCID: PMC9888523 DOI: 10.1038/s41559-022-01829-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 06/15/2022] [Indexed: 02/02/2023]
Abstract
The origin of snake venom involved duplication and recruitment of non-venom genes into venom systems. Several studies have predicted that directional positive selection has governed this process. Venom composition varies substantially across snake species and venom phenotypes are locally adapted to prey, leading to coevolutionary interactions between predator and prey. Venom origins and contemporary snake venom evolution may therefore be driven by fundamentally different selection regimes, yet investigations of population-level patterns of selection have been limited. Here, we use whole-genome data from 68 rattlesnakes to test hypotheses about the factors that drive genomic diversity and differentiation in major venom gene regions. We show that selection has resulted in long-term maintenance of genetic diversity within and between species in multiple venom gene families. Our findings are inconsistent with a dominant role of directional positive selection and instead support a role of long-term balancing selection in shaping venom evolution. We also detect rapid decay of linkage disequilibrium due to high recombination rates in venom regions, suggesting that venom genes have reduced selective interference with nearby loci, including other venom paralogues. Our results provide an example of long-term balancing selection that drives trans-species polymorphism and help to explain how snake venom keeps pace with prey resistance.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Richard H Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
| | | | | | | | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Joshua M Parker
- Life Science Department, Fresno City College, Fresno, CA, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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32
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Jeong H, Baran NM, Sun D, Chatterjee P, Layman TS, Balakrishnan CN, Maney DL, Yi SV. Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows. eLife 2022; 11:e79387. [PMID: 36040313 PMCID: PMC9427109 DOI: 10.7554/elife.79387] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/17/2022] [Indexed: 12/11/2022] Open
Abstract
In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of 'supergenes.' Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2m chromosomes in this species. We found that features of ZAL2m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.
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Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Nicole M Baran
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Department of Psychology, Emory UniversityAtlantaUnited States
- Department of Ecology, Evolution, Marine Biology, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Dan Sun
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Department of Medicine Huddinge, Karolinska InstitutetStockholmSweden
| | - Paramita Chatterjee
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Thomas S Layman
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | | | - Donna L Maney
- Department of Psychology, Emory UniversityAtlantaUnited States
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
- Department of Ecology, Evolution, Marine Biology, University of California, Santa BarbaraSanta BarbaraUnited States
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33
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Maldonado JA, Firneno TJ, Hall AS, Fujita MK. Parthenogenesis doubles the rate of amino acid substitution in whiptail mitochondria. Evolution 2022; 76:1434-1442. [PMID: 35580923 DOI: 10.1111/evo.14509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/10/2022] [Accepted: 03/21/2022] [Indexed: 01/21/2023]
Abstract
Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the dN/dS ratios in asexual vertebrate lineages in the genus Aspidoscelis using whole mitochondrial genomes from seven asexual and five sexual species. We found higher dN/dS ratios in asexual Aspidoscelis species, indicating that asexual whiptails accumulate nonsynonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provide empirical evidence to corroborate the connection between asexuality and increased amino acid substitutions in asexual vertebrate lineages.
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Affiliation(s)
- Jose A Maldonado
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Thomas J Firneno
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Alexander S Hall
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, The University of Texas, Arlington, Texas, USA
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34
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Chen DS, Clark AG, Wolfner MF. Octopaminergic/tyraminergic Tdc2 neurons regulate biased sperm usage in female Drosophila melanogaster. Genetics 2022; 221:6613932. [PMID: 35736370 DOI: 10.1093/genetics/iyac097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/04/2022] [Indexed: 11/14/2022] Open
Abstract
In polyandrous internally fertilizing species, a multiply-mated female can use stored sperm from different males in a biased manner to fertilize her eggs. The female's ability to assess sperm quality and compatibility is essential for her reproductive success, and represents an important aspect of postcopulatory sexual selection. In Drosophila melanogaster, previous studies demonstrated that the female nervous system plays an active role in influencing progeny paternity proportion, and suggested a role for octopaminergic/tyraminergic Tdc2 neurons in this process. Here, we report that inhibiting Tdc2 neuronal activity causes females to produce a higher-than-normal proportion of first-male progeny. This difference is not due to differences in sperm storage or release, but instead is attributable to the suppression of second-male sperm usage bias that normally occurs in control females. We further show that a subset of Tdc2 neurons innervating the female reproductive tract is largely responsible for the progeny proportion phenotype that is observed when Tdc2 neurons are inhibited globally. On the contrary, overactivation of Tdc2 neurons does not further affect sperm storage and release or progeny proportion. These results suggest that octopaminergic/tyraminergic signaling allows a multiply-mated female to bias sperm usage, and identify a new role for the female nervous system in postcopulatory sexual selection.
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Affiliation(s)
- Dawn S Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14853, USA
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14853, USA
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35
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Schreiber M, Gao Y, Koch N, Fuchs J, Heckmann S, Himmelbach A, Börner A, Özkan H, Maurer A, Stein N, Mascher M, Dreissig S. Recombination landscape divergence between populations is marked by larger low-recombining regions in domesticated rye. Mol Biol Evol 2022; 39:msac131. [PMID: 35687854 PMCID: PMC9218680 DOI: 10.1093/molbev/msac131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The genomic landscape of recombination plays an essential role in evolution. Patterns of recombination are highly variable along chromosomes, between sexes, individuals, populations, and species. In many eukaryotes, recombination rates are elevated in sub-telomeric regions and drastically reduced near centromeres, resulting in large low-recombining (LR) regions. The processes of recombination are influenced by genetic factors, such as different alleles of genes involved in meiosis and chromatin structure, as well as external environmental stimuli like temperature and overall stress. In this work, we focused on the genomic landscapes of recombination in a collection of 916 rye (Secale cereale) individuals. By analysing population structure among individuals of different domestication status and geographic origin, we detected high levels of admixture, reflecting the reproductive biology of a self-incompatible, wind-pollinating grass species. We then analysed patterns of recombination in overlapping subpopulations, which revealed substantial variation in the physical size of LR regions, with a tendency for larger LR regions in domesticated subpopulations. Genome-wide association scans (GWAS) for LR region size revealed a major quantitative-trait-locus (QTL) at which, among 18 annotated genes, an ortholog of histone H4 acetyltransferase ESA1 was located. Rye individuals belonging to domesticated subpopulations showed increased synaptonemal complex length, but no difference in crossover frequency, indicating that only the recombination landscape is different. Furthermore, the genomic region harbouring rye ScESA1 showed moderate patterns of selection in domesticated subpopulations, suggesting that larger LR regions were indirectly selected for during domestication to achieve more homogeneous populations for agricultural use.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, 35037 Marburg, Germany
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Yixuan Gao
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Natalie Koch
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Stefan Heckmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Hakan Özkan
- Faculty of Agriculture, Department of Field Crops, University of Cukurova, 01330 Adana, Turkey
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Steven Dreissig
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
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Kearney MR, Jasper ME, White VL, Aitkenhead IJ, Blacket MJ, Kong JD, Chown SL, Hoffmann AA. Parthenogenesis without costs in a grasshopper with hybrid origins. Science 2022; 376:1110-1114. [PMID: 35653484 DOI: 10.1126/science.abm1072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The rarity of parthenogenetic species is typically attributed to the reduced genetic variability that accompanies the absence of sex, yet natural parthenogens can be surprisingly successful. Ecological success is often proposed to derive from hybridization through enhanced genetic diversity from repetitive origins or enhanced phenotypic breadth from heterosis. Here, we tested and rejected both hypotheses in a classic parthenogen, the diploid grasshopper Warramaba virgo. Genetic data revealed a single hybrid mating origin at least 0.25 million years ago, and comparative analyses of 14 physiological and life history traits showed no evidence for altered fitness relative to its sexual progenitors. Our findings imply that the rarity of parthenogenesis is due to constraints on origin rather than to rapid extinction.
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Affiliation(s)
- Michael R Kearney
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Moshe E Jasper
- Bio21 Institute, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Vanessa L White
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Ian J Aitkenhead
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Mark J Blacket
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Jacinta D Kong
- School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Victoria 3800, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
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37
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Kim H, Choi K. Fast and Precise: How to Measure Meiotic Crossovers in Arabidopsis. Mol Cells 2022; 45:273-283. [PMID: 35444069 PMCID: PMC9095510 DOI: 10.14348/molcells.2022.2054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/21/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022] Open
Abstract
During meiosis, homologous chromosomes (homologs) pair and undergo genetic recombination via assembly and disassembly of the synaptonemal complex. Meiotic recombination is initiated by excess formation of DNA double-strand breaks (DSBs), among which a subset are repaired by reciprocal genetic exchange, called crossovers (COs). COs generate genetic variations across generations, profoundly affecting genetic diversity and breeding. At least one CO between homologs is essential for the first meiotic chromosome segregation, but generally only one and fewer than three inter-homolog COs occur in plants. CO frequency and distribution are biased along chromosomes, suppressed in centromeres, and controlled by pro-CO, anti-CO, and epigenetic factors. Accurate and high-throughput detection of COs is important for our understanding of CO formation and chromosome behavior. Here, we review advanced approaches that enable precise measurement of the location, frequency, and genomic landscapes of COs in plants, with a focus on Arabidopsis thaliana.
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Affiliation(s)
- Heejin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Kyuha Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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Brekke C, Berg P, Gjuvsland AB, Johnston SE. Recombination rates in pigs differ between breeds, sexes and individuals, and are associated with the RNF212, SYCP2, PRDM7, MEI1 and MSH4 loci. Genet Sel Evol 2022; 54:33. [PMID: 35596132 PMCID: PMC9123673 DOI: 10.1186/s12711-022-00723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Background Recombination is a fundamental part of mammalian meiosis that leads to the exchange of large segments of DNA between homologous chromosomes and is therefore an important driver of genetic diversity in populations. In breeding populations, understanding recombination is of particular interest because it can break up unfavourable linkage phases between alleles and produce novel combinations of alleles that could be exploited in selection. In this study, we used dense single nucleotide polymorphism (SNP) genotype data and pedigree information to analyse individual and sex-specific variation and genetic architecture of recombination rates within and between five commercially selected pig breeds. Results In agreement with previous studies, recombination rates were higher in females than in males for all breeds and for all chromosomes, except 1 and 13, for which male rates were slightly higher. Total recombination rate differed between breeds but the pattern of recombination along the chromosomes was well conserved across breeds for the same sex. The autosomal linkage maps spanned a total length of 1731 to 1887 cM for males and of 2231 to 2515 cM for females. Estimates of heritability for individual autosomal crossover count ranged from 0.04 to 0.07 for males and from 0.08 to 0.11 for females. Fourteen genomic regions were found to be associated with individual autosomal crossover count. Of these, four were close to or within candidate genes that have previously been associated with individual recombination rates in pigs and other mammals, namely RNF212, SYCP2 and MSH4. Two of the identified regions included the PRDM7 and MEI1 genes, which are known to be involved in meiosis but have not been previously associated with variation in individual recombination rates. Conclusions This study shows that genetic variation in autosomal recombination rate persists in domesticated species under strong selection, with differences between closely-related breeds and marked differences between the sexes. Our findings support results from other studies, i.e., that individual crossover counts are associated with the RNF212, SYCP2 and MSH4 genes in pig. In addition, we have found two novel candidate genes associated with the trait, namely PRDM7 and MEI1. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00723-9.
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Affiliation(s)
- Cathrine Brekke
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433, Ås, Norway.
| | - Peer Berg
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433, Ås, Norway
| | | | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
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El-Ganainy SM, Iqbal Z, Awad HM, Sattar MN, Tohamy AM, Abbas AO, Squires J, Cooke DEL. Genotypic and Phenotypic Structure of the Population of Phytophthora infestans in Egypt Revealed the Presence of European Genotypes. J Fungi (Basel) 2022; 8:jof8050468. [PMID: 35628724 PMCID: PMC9147654 DOI: 10.3390/jof8050468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/10/2022] Open
Abstract
Late blight disease of potato and tomato, caused by Phytophthora infestans, results in serious losses to Egyptian and global potato and tomato production. To understand the structure and dynamics of the Egyptian population of P. infestans, 205 isolates were collected from potato and tomato plants during three growing seasons in 2010–2012. The characterization was achieved by mating-type assay, metalaxyl sensitivity assay, and virulence pattern. Additionally, genotyping of 85 Egyptian isolates and 15 reference UK isolates was performed using 12 highly informative microsatellite (SSR) markers David E. L. Cooke and five effector (RxLR) genes. Mating-type testing showed that 58% (118 of 205) of the isolates belonged to mating type A1, 35% (71 isolates) to mating type A2, and the rest 8% (16 isolates) were self-fertile. The phenotype of metalaxyl response was represented as 45% resistant, 43% sensitive, and 12% as intermediate. Structure analysis grouped the 85 identified genotypes into two main clonal lineages. The first clonal lineage comprised 21 isolates belonging to A2 mating type and 8 self-fertile isolates. This clonal lineage was identified as Blue_13 or EU_13_A2. The second main clonal lineage comprised 55 isolates and was identified as EU_23_A1. A single isolate with a novel SSR genotype that formed a distinct genetic grouping was also identified. The effector sequencing showed good correspondence with the virulence data and highlighted differences in the presence and absence of loci as well as nucleotide polymorphism that affect gene function. This study indicated a changing population of P. infestans in Egypt and discusses the findings in the context of late blight management.
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Affiliation(s)
- Sherif Mohamed El-Ganainy
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
| | - Zafar Iqbal
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Hossam Mohamed Awad
- Agriculture Botany Department, Menofia University, Shibin El-Kom 32415, Egypt;
| | - Muhammad Naeem Sattar
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (Z.I.); (M.N.S.)
| | - Abdel Mohsen Tohamy
- Vegetable Diseases Research Department, Plant Pathology Research Institute, ARC, Giza 12619, Egypt;
| | - Ahmed O. Abbas
- Department of Animal and Fish Production, College of Agricultural and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia;
| | | | - David E. L. Cooke
- The James Hutton Institute, Dundee DD2 5DA, UK;
- Correspondence: (S.M.E.-G.); (D.E.L.C.)
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Akopyan M, Tigano A, Jacobs A, Wilder AP, Baumann H, Therkildsen NO. Comparative linkage mapping uncovers recombination suppression across massive chromosomal inversions associated with local adaptation in Atlantic silversides. Mol Ecol 2022; 31:3323-3341. [DOI: 10.1111/mec.16472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/28/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Maria Akopyan
- Department of Ecology and Evolutionary Biology Cornell University NY USA
| | - Anna Tigano
- Department of Biology UBC Okanagan Campus British Columbia Canada
- Department of Natural Resources and the Environment Cornell University NY USA
| | - Arne Jacobs
- Institute of Biodiversity Animal Health & Comparative Medicine University of Glasgow UK
- Department of Natural Resources and the Environment Cornell University NY USA
| | - Aryn P. Wilder
- Conservation Science Wildlife Health San Diego Zoo Wildlife Alliance CA USA
- Department of Natural Resources and the Environment Cornell University NY USA
| | - Hannes Baumann
- Department of Marine Sciences University of Connecticut CT USA
| | - Nina O. Therkildsen
- Department of Natural Resources and the Environment Cornell University NY USA
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Foe VE. Does the Pachytene Checkpoint, a Feature of Meiosis, Filter Out Mistakes in Double-Strand DNA Break Repair and as a side-Effect Strongly Promote Adaptive Speciation? Integr Org Biol 2022; 4:obac008. [PMID: 36827645 PMCID: PMC8998493 DOI: 10.1093/iob/obac008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This essay aims to explain two biological puzzles: why eukaryotic transcription units are composed of short segments of coding DNA interspersed with long stretches of non-coding (intron) DNA, and the near ubiquity of sexual reproduction. As is well known, alternative splicing of its coding sequences enables one transcription unit to produce multiple variants of each encoded protein. Additionally, padding transcription units with non-coding DNA (often many thousands of base pairs long) provides a readily evolvable way to set how soon in a cell cycle the various mRNAs will begin being expressed and the total amount of mRNA that each transcription unit can make during a cell cycle. This regulation complements control via the transcriptional promoter and facilitates the creation of complex eukaryotic cell types, tissues, and organisms. However, it also makes eukaryotes exceedingly vulnerable to double-strand DNA breaks, which end-joining break repair pathways can repair incorrectly. Transcription units cover such a large fraction of the genome that any mis-repair producing a reorganized chromosome has a high probability of destroying a gene. During meiosis, the synaptonemal complex aligns homologous chromosome pairs and the pachytene checkpoint detects, selectively arrests, and in many organisms actively destroys gamete-producing cells with chromosomes that cannot adequately synapse; this creates a filter favoring transmission to the next generation of chromosomes that retain the parental organization, while selectively culling those with interrupted transcription units. This same meiotic checkpoint, reacting to accidental chromosomal reorganizations inflicted by error-prone break repair, can, as a side effect, provide a mechanism for the formation of new species in sympatry. It has been a long-standing puzzle how something as seemingly maladaptive as hybrid sterility between such new species can arise. I suggest that this paradox is resolved by understanding the adaptive importance of the pachytene checkpoint, as outlined above.
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Panov A, Mayorov VI, Dikalov S. Metabolic Syndrome and β-Oxidation of Long-Chain Fatty Acids in the Brain, Heart, and Kidney Mitochondria. Int J Mol Sci 2022; 23:4047. [PMID: 35409406 PMCID: PMC9000033 DOI: 10.3390/ijms23074047] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
We present evidence that metabolic syndrome (MetS) represents the postreproductive stage of the human postembryonic ontogenesis. Accordingly, the genes governing this stage experience relatively weak evolutionary selection pressure, thus representing the metabolic phenotype of distant ancestors with β-oxidation of long-chain fatty acids (FAs) as the primary energy source. Mitochondria oxidize at high-rate FAs only when succinate, glutamate, or pyruvate are present. The heart and brain mitochondria work at a wide range of functional loads and possess an intrinsic inhibition of complex II to prevent oxidative stress at periods of low functional activity. Kidney mitochondria constantly work at a high rate and lack inhibition of complex II. We suggest that in people with MetS, oxidative stress is the central mechanism of the heart and brain pathologies. Oxidative stress is a secondary pathogenetic mechanism in the kidney, while the primary mechanisms are kidney hypoxia caused by persistent hyperglycemia and hypertension. Current evidence suggests that most of the nongenetic pathologies associated with MetS originate from the inconsistencies between the metabolic phenotype acquired after the transition to the postreproductive stage and excessive consumption of food rich in carbohydrates and a sedentary lifestyle.
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Affiliation(s)
- Alexander Panov
- Department of Biomedical Sciences, Mercer University School of Medicine, Macon, GA 31201, USA;
| | - Vladimir I. Mayorov
- Department of Biomedical Sciences, Mercer University School of Medicine, Macon, GA 31201, USA;
| | - Sergey Dikalov
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
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Yang L, Gao Y, Li M, Park KE, Liu S, Kang X, Liu M, Oswalt A, Fang L, Telugu BP, Sattler CG, Li CJ, Cole JB, Seroussi E, Xu L, Yang L, Zhou Y, Li L, Zhang H, Rosen BD, Van Tassell CP, Ma L, Liu GE. Genome-wide recombination map construction from single sperm sequencing in cattle. BMC Genomics 2022; 23:181. [PMID: 35247961 PMCID: PMC8898482 DOI: 10.1186/s12864-022-08415-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Meiotic recombination is one of the important phenomena contributing to gamete genome diversity. However, except for human and a few model organisms, it is not well studied in livestock, including cattle. RESULTS To investigate their distributions in the cattle sperm genome, we sequenced 143 single sperms from two Holstein bulls. We mapped meiotic recombination events at high resolution based on phased heterozygous single nucleotide polymorphism (SNP). In the absence of evolutionary selection pressure in fertilization and survival, recombination events in sperm are enriched near distal chromosomal ends, revealing that such a pattern is intrinsic to the molecular mechanism of meiosis. Furthermore, we further validated these findings in single sperms with results derived from sequencing its family trio of diploid genomes and our previous studies of recombination in cattle. CONCLUSIONS To our knowledge, this is the first large-scale single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of recombination, genome instability, and male infertility.
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Affiliation(s)
- Liu Yang
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Mingxun Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009 China
| | - Ki-Eun Park
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xiaolong Kang
- College of Agriculture, Ningxia University, Yinchuan, 750021 China
| | - Mei Liu
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128 China
| | - Adam Oswalt
- Select Sires Inc, 11740 U.S. 42 North, Plain City, OH 43064 USA
| | - Lingzhao Fang
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - Bhanu P. Telugu
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
- Division of Animal Sciences, University of Missouri, Columbia, MO 65201 USA
| | | | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, P.O.B 15159, HaMaccabim Road, 7528809 Rishon LeTsiyon, Israel
| | - Lingyang Xu
- Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130 China
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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Chan AW, Villwock SS, Williams AL, Jannink JL. Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm. G3 (BETHESDA, MD.) 2022; 12:jkab372. [PMID: 34791172 PMCID: PMC8728042 DOI: 10.1093/g3journal/jkab372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 09/29/2021] [Indexed: 01/09/2023]
Abstract
Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing data and a validated multigenerational pedigree from the International Institute of Tropical Agriculture cassava breeding germplasm consisting of 7020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium. We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.
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Affiliation(s)
- Ariel W Chan
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Seren S Villwock
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Amy L Williams
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jean-Luc Jannink
- RW Holley Center for Agriculture and Health, United States Department of Agriculture—Agricultural Research Service, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
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45
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Ye Z, Jiang X, Pfrender ME, Lynch M. Genome-Wide Allele-Specific Expression in Obligately Asexual Daphnia pulex and the Implications for the Genetic Basis of Asexuality. Genome Biol Evol 2021; 13:6415829. [PMID: 34726699 PMCID: PMC8598174 DOI: 10.1093/gbe/evab243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/17/2023] Open
Abstract
Although obligately asexual lineages are thought to experience selective disadvantages associated with reduced efficiency of fixing beneficial mutations and purging deleterious mutations, such lineages are phylogenetically and geographically widespread. However, despite several genome-wide association studies, little is known about the genetic elements underlying the origin of obligate asexuality and how they spread. Because many obligately asexual lineages have hybrid origins, it has been suggested that asexuality is caused by the unbalanced expression of alleles from the hybridizing species. Here, we investigate this idea by identifying genes with allele-specific expression (ASE) in a Daphnia pulex population, in which obligate parthenogens (OP) and cyclical parthenogens (CP) coexist, with the OP clones having been originally derived from hybridization between CP D. pulex and its sister species, Daphnia pulicaria. OP D. pulex have significantly more ASE genes (ASEGs) than do CP D. pulex. Whole-genomic comparison of OP and CP clones revealed ∼15,000 OP-specific markers and 42 consistent ASEGs enriched in marker-defined regions. Ten of the 42 ASEGs have alleles coding for different protein sequences, suggesting functional differences between the products of the two parental alleles. At least three of these ten genes appear to be directly involved in meiosis-related processes, for example, RanBP2 can cause abnormal chromosome segregation in anaphase I, and the presence of Wee1 in immature oocytes leads to failure to enter meiosis II. These results provide a guide for future molecular resolution of the genetic basis of the transition to ameiotic parthenogenesis.
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Affiliation(s)
- Zhiqiang Ye
- Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
| | | | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana
| | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona
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Gavin‐Smyth N, Kramer AT, Urbina‐Casanova R, Vitt P, Fant JB. Genetic rescue reduces mate limitation in a threatened, clonal, and self‐incompatible plant species. Restor Ecol 2021. [DOI: 10.1111/rec.13458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nora Gavin‐Smyth
- Plant Biology and Conservation Northwestern University Evanston IL 60201 U.S.A
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Glencoe IL 60022 U.S.A
| | - Andrea T. Kramer
- Plant Biology and Conservation Northwestern University Evanston IL 60201 U.S.A
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Glencoe IL 60022 U.S.A
| | - Rafael Urbina‐Casanova
- Plant Biology and Conservation Northwestern University Evanston IL 60201 U.S.A
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Glencoe IL 60022 U.S.A
| | - Pati Vitt
- Plant Biology and Conservation Northwestern University Evanston IL 60201 U.S.A
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Glencoe IL 60022 U.S.A
- Lake County Forest Preserve District 1899 W. Winchester Road, Libertyville IL 60048 U.S.A
| | - Jeremie B. Fant
- Plant Biology and Conservation Northwestern University Evanston IL 60201 U.S.A
- Negaunee Institute for Plant Conservation Science and Action Chicago Botanic Garden Glencoe IL 60022 U.S.A
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Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proc Biol Sci 2021; 288:20211720. [PMID: 34547909 PMCID: PMC8456138 DOI: 10.1098/rspb.2021.1720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/31/2021] [Indexed: 11/12/2022] Open
Abstract
While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.
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Affiliation(s)
- Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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Mezhzherin SV, Chayka YY, Vlasenko RP, Zhalay OI, Garbar OV. The Genetic Structure Features of the Amphimictic Earthworm Aporrectodea caliginosa (Oligochaeta, Lumbricidae) Populations within Ukraine. CYTOL GENET+ 2021. [DOI: 10.3103/s009545272105008x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tock AJ, Holland DM, Jiang W, Osman K, Sanchez-Moran E, Higgins JD, Edwards KJ, Uauy C, Franklin FCH, Henderson IR. Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation. Genome Res 2021; 31:1614-1628. [PMID: 34426514 PMCID: PMC8415368 DOI: 10.1101/gr.273672.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 07/20/2021] [Indexed: 12/18/2022]
Abstract
The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host–pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.
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Affiliation(s)
- Andrew J Tock
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Daniel M Holland
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Wei Jiang
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Kim Osman
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | | | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Keith J Edwards
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | | | - F Chris H Franklin
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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50
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Natural variation identifies SNI1, the SMC5/6 component, as a modifier of meiotic crossover in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2021970118. [PMID: 34385313 PMCID: PMC8379953 DOI: 10.1073/pnas.2021970118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination plays a fundamental role in shaping genetic diversity in eukaryotes. Extensive variation in crossover rate exists between populations and species. The identity of modifier loci and their roles in genome evolution remain incompletely understood. We explored natural variation in Arabidopsis crossover and identified SNI1 as the causal gene underlying a major modifier locus. To date, SNI1 had no known role in crossover. SNI1 is a component of the SMC5/6 complex that is closely related to cohesin and condensin. Arabidopsis sni1 and other SMC5/6 mutants show similar effects on the interference-independent crossover pathway. Hence, our findings demonstrate that the SMC5/6 complex, which is known for its role in DNA damage repair, is also important for control of meiotic crossover. The frequency and distribution of meiotic crossovers are tightly controlled; however, variation in this process can be observed both within and between species. Using crosses of two natural Arabidopsis thaliana accessions, Col and Ler, we mapped a crossover modifier locus to semidominant polymorphisms in SUPPRESSOR OF NPR1-1 INDUCIBLE 1 (SNI1), which encodes a component of the SMC5/6 complex. The sni1 mutant exhibits a modified pattern of recombination across the genome with crossovers elevated in chromosome distal regions but reduced in pericentromeres. Mutations in SNI1 result in reduced crossover interference and can partially restore the fertility of a Class I crossover pathway mutant, which suggests that the protein affects noninterfering crossover repair. Therefore, we tested genetic interactions between SNI1 and both RECQ4 and FANCM DNA helicases, which showed that additional Class II crossovers observed in the sni1 mutant are FANCM independent. Furthermore, genetic analysis of other SMC5/6 mutants confirms the observations of crossover redistribution made for SNI1. The study reveals the importance of the SMC5/6 complex in ensuring the proper progress of meiotic recombination in plants.
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