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Palahí I Torres A, Höök L, Näsvall K, Shipilina D, Wiklund C, Vila R, Pruisscher P, Backström N. The fine-scale recombination rate variation and associations with genomic features in a butterfly. Genome Res 2023; 33:810-823. [PMID: 37308293 PMCID: PMC10317125 DOI: 10.1101/gr.277414.122] [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: 10/19/2022] [Accepted: 05/03/2023] [Indexed: 06/14/2023]
Abstract
Recombination is a key molecular mechanism that has profound implications on both micro- and macroevolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, in particular in Lepidoptera (moths and butterflies). The wood white butterfly (Leptidea sinapis) shows considerable intraspecific variation in chromosome numbers and is a suitable system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole-genome resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed that larger chromosomes had a bimodal recombination landscape, potentially caused by interference between simultaneous chiasmata. The recombination rate was significantly lower in subtelomeric regions, with exceptions associated with segregating chromosome rearrangements, showing that fissions and fusions can have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a limited influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity in recombination coldspots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and have particular implications for forthcoming research in population genetics, molecular/genome evolution, and speciation.
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Affiliation(s)
- Aleix Palahí I Torres
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden;
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Christer Wiklund
- Department of Zoology: Division of Ecology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Roger Vila
- Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
| | - Peter Pruisscher
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden
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2
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Huang Y, Roig I. Genetic control of meiosis surveillance mechanisms in mammals. Front Cell Dev Biol 2023; 11:1127440. [PMID: 36910159 PMCID: PMC9996228 DOI: 10.3389/fcell.2023.1127440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Meiosis is a specialized cell division that generates haploid gametes and is critical for successful sexual reproduction. During the extended meiotic prophase I, homologous chromosomes progressively pair, synapse and desynapse. These chromosomal dynamics are tightly integrated with meiotic recombination (MR), during which programmed DNA double-strand breaks (DSBs) are formed and subsequently repaired. Consequently, parental chromosome arms reciprocally exchange, ultimately ensuring accurate homolog segregation and genetic diversity in the offspring. Surveillance mechanisms carefully monitor the MR and homologous chromosome synapsis during meiotic prophase I to avoid producing aberrant chromosomes and defective gametes. Errors in these critical processes would lead to aneuploidy and/or genetic instability. Studies of mutation in mouse models, coupled with advances in genomic technologies, lead us to more clearly understand how meiosis is controlled and how meiotic errors are linked to mammalian infertility. Here, we review the genetic regulations of these major meiotic events in mice and highlight our current understanding of their surveillance mechanisms. Furthermore, we summarize meiotic prophase genes, the mutations that activate the surveillance system leading to meiotic prophase arrest in mouse models, and their corresponding genetic variants identified in human infertile patients. Finally, we discuss their value for the diagnosis of causes of meiosis-based infertility in humans.
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Affiliation(s)
- Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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3
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Taniguti CH, Taniguti LM, Amadeu RR, Lau J, Gesteira GDS, Oliveira TDP, Ferreira GC, Pereira GDS, Byrne D, Mollinari M, Riera-Lizarazu O, Garcia AAF. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. Gigascience 2022; 12:giad092. [PMID: 37889010 PMCID: PMC10603770 DOI: 10.1093/gigascience/giad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/27/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations. RESULTS We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent). CONCLUSIONS We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.
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Affiliation(s)
- Cristiane Hayumi Taniguti
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Lucas Mitsuo Taniguti
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Mendelics Genomic Analysis, São Paulo 02511-000, Brazil
| | | | - Jeekin Lau
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Gabriel de Siqueira Gesteira
- Department of Genetics, University of São Paulo, São Paulo 13418-900, Brazil
- Bioinformatics Research Center, Department of Horticultural Sciences, North Carolina State University, Raleigh, NC 27695-7566, USA
| | | | | | | | - David Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
| | - Marcelo Mollinari
- Bioinformatics Research Center, Department of Horticultural Sciences, North Carolina State University, Raleigh, NC 27695-7566, USA
| | - Oscar Riera-Lizarazu
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-0001, USA
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Shipilina D, Näsvall K, Höök L, Vila R, Talavera G, Backström N. Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly. Genomics 2022; 114:110481. [PMID: 36115505 DOI: 10.1016/j.ygeno.2022.110481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/14/2023]
Abstract
Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden; Swedish Collegium for Advanced Study, Thunbergsvägen 2, 75236 Uppsala, Sweden.
| | - Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Roger Vila
- The Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva, Passeig Martim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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5
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Sen S, Dodamani A, Nambiar M. Emerging mechanisms and roles of meiotic crossover repression at centromeres. Curr Top Dev Biol 2022; 151:155-190. [PMID: 36681469 DOI: 10.1016/bs.ctdb.2022.06.003] [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: 01/25/2023]
Abstract
Crossover events during recombination in meiosis are essential for generating genetic diversity as well as crucial to allow accurate chromosomal segregation between homologous chromosomes. Spatial control for the distribution of crossover events along the chromosomes is largely a tightly regulated process and involves many facets such as interference, repression as well as assurance, to make sure that not too many or too few crossovers are generated. Repression of crossover events at the centromeres is a highly conserved process across all species tested. Failure to inhibit such recombination events can result in chromosomal mis-segregation during meiosis resulting in aneuploid gametes that are responsible for infertility or developmental disorders such as Down's syndrome and other trisomies in humans. In the past few decades, studies to understand the molecular mechanisms behind this repression have shown the involvement of a multitude of factors ranging from the centromere-specific proteins such as the kinetochore to the flanking pericentric heterochromatin as well as DNA double-strand break repair pathways. In this chapter, we review the different mechanisms of pericentric repression mechanisms known till date as well as highlight the importance of understanding this regulation in the context of chromosomal segregation defects. We also discuss the clinical implications of dysregulation of this process, especially in human reproductive health and genetic diseases.
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Affiliation(s)
- Sucharita Sen
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Ananya Dodamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Mridula Nambiar
- Department of Biology, Indian Institute of Science Education and Research, Pune, India.
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6
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Xie C, Wang W, Tu C, Meng L, Lu G, Lin G, Lu LY, Tan YQ. OUP accepted manuscript. Hum Reprod Update 2022; 28:763-797. [PMID: 35613017 DOI: 10.1093/humupd/dmac024] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/18/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chunbo Xie
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Weili Wang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Chaofeng Tu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lanlan Meng
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Guangxiu Lu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ge Lin
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lin-Yu Lu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue-Qiu Tan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
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7
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Abstract
We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites, which are credited as the genetic and genomic definition of human centromeres due to their interaction with inner kinetochore proteins and their importance in the development of human artificial chromosome assays. We provide an overview of alpha satellite repeat structure and array organization in the context of these high-quality reference data sets; discuss the emergence of variation-based surveys; and provide perspective on the role of this new source of genetic and epigenetic variation in the context of chromosome biology, genome instability, and human disease.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; .,Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ivan A Alexandrov
- Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; .,Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg 199004, Russia.,Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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8
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Pazhayam NM, Turcotte CA, Sekelsky J. Meiotic Crossover Patterning. Front Cell Dev Biol 2021; 9:681123. [PMID: 34368131 PMCID: PMC8344875 DOI: 10.3389/fcell.2021.681123] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/28/2021] [Indexed: 12/02/2022] Open
Abstract
Proper number and placement of meiotic crossovers is vital to chromosome segregation, with failures in normal crossover distribution often resulting in aneuploidy and infertility. Meiotic crossovers are formed via homologous repair of programmed double-strand breaks (DSBs). Although DSBs occur throughout the genome, crossover placement is intricately patterned, as observed first in early genetic studies by Muller and Sturtevant. Three types of patterning events have been identified. Interference, first described by Sturtevant in 1915, is a phenomenon in which crossovers on the same chromosome do not occur near one another. Assurance, initially identified by Owen in 1949, describes the phenomenon in which a minimum of one crossover is formed per chromosome pair. Suppression, first observed by Beadle in 1932, dictates that crossovers do not occur in regions surrounding the centromere and telomeres. The mechanisms behind crossover patterning remain largely unknown, and key players appear to act at all scales, from the DNA level to inter-chromosome interactions. There is also considerable overlap between the known players that drive each patterning phenomenon. In this review we discuss the history of studies of crossover patterning, developments in methods used in the field, and our current understanding of the interplay between patterning phenomena.
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Affiliation(s)
- Nila M. Pazhayam
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Carolyn A. Turcotte
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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9
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Abstract
The presence of meiosis, which is a conserved component of sexual reproduction, across organisms from all eukaryotic kingdoms, strongly argues that sex is a primordial feature of eukaryotes. However, extant meiotic structures and processes can vary considerably between organisms. The ciliated protist Tetrahymena thermophila, which diverged from animals, plants, and fungi early in evolution, provides one example of a rather unconventional meiosis. Tetrahymena has a simpler meiosis compared with most other organisms: It lacks both a synaptonemal complex (SC) and specialized meiotic machinery for chromosome cohesion and has a reduced capacity to regulate meiotic recombination. Despite this, it also features several unique mechanisms, including elongation of the nucleus to twice the cell length to promote homologous pairing and prevent recombination between sister chromatids. Comparison of the meiotic programs of Tetrahymena and higher multicellular organisms may reveal how extant meiosis evolved from proto-meiosis.
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Affiliation(s)
- Josef Loidl
- Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
- * E-mail:
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10
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Sims J, Schlögelhofer P, Kurzbauer MT. From Microscopy to Nanoscopy: Defining an Arabidopsis thaliana Meiotic Atlas at the Nanometer Scale. FRONTIERS IN PLANT SCIENCE 2021; 12:672914. [PMID: 34084178 PMCID: PMC8167036 DOI: 10.3389/fpls.2021.672914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Visualization of meiotic chromosomes and the proteins involved in meiotic recombination have become essential to study meiosis in many systems including the model plant Arabidopsis thaliana. Recent advances in super-resolution technologies changed how microscopic images are acquired and analyzed. New technologies enable observation of cells and nuclei at a nanometer scale and hold great promise to the field since they allow observing complex meiotic molecular processes with unprecedented detail. Here, we provide an overview of classical and advanced sample preparation and microscopy techniques with an updated Arabidopsis meiotic atlas based on super-resolution microscopy. We review different techniques, focusing on stimulated emission depletion (STED) nanoscopy, to offer researchers guidance for selecting the optimal protocol and equipment to address their scientific question.
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11
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Lin M, Lv J, Zhao D, Liu S, Xu J, Wu Y, Wang F, Zhang J, Zheng B, Shen C, Guan X, Yu J, Huang X. MRNIP is essential for meiotic progression and spermatogenesis in mice. Biochem Biophys Res Commun 2021; 550:127-133. [PMID: 33689881 DOI: 10.1016/j.bbrc.2021.02.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 02/27/2021] [Indexed: 12/14/2022]
Abstract
Meiotic homologous recombination (HR) initiates with the programmed generation of DNA double-strand breaks (DSBs), which result in the exchange of genetic information and genome diversity. This process requires the tight cooperation of the MRE11-RAD50-NBS1 (MRN) complex to promote DSB formation and DNA end resection. However, the mechanism regulating MRN complex remains to be explored. In the present study, we report that MRN-interacting protein, MRNIP, is a novel factor for HR and is crucial for the expression of the MRN complex and loading of recombinases DMC1/RAD51. Knockout of Mrnip in mice led to aberrant synapsis, impaired HR, and male subfertility. In conclusion, MRNIP is a novel HR factor that probably promotes meiotic progression through the MRN complex.
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Affiliation(s)
- Meng Lin
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Jinxing Lv
- Suzhou Dushu Lake Hospital (Dushu Lake Hospital Affiliated to Soochow University), Suzhou, China
| | - Dan Zhao
- Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Siyu Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Jinfu Xu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Yangyang Wu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Fuxin Wang
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Bo Zheng
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China
| | - Cong Shen
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, Suzhou, China.
| | - Xie Guan
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China.
| | - Jun Yu
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China.
| | - Xiaoyan Huang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
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12
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Ferreira MTM, Glombik M, Perničková K, Duchoslav M, Scholten O, Karafiátová M, Techio VH, Doležel J, Lukaszewski AJ, Kopecký D. Direct evidence for crossover and chromatid interference in meiosis of two plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei). JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:254-267. [PMID: 33029645 PMCID: PMC7853598 DOI: 10.1093/jxb/eraa455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/05/2020] [Indexed: 05/02/2023]
Abstract
Crossing over, in addition to its strictly genetic role, also performs a critical mechanical function, by bonding homologues in meiosis. Hence, it is responsible for an orderly reduction of the chromosome number. As such, it is strictly controlled in frequency and distribution. The well-known crossover control is positive crossover interference which reduces the probability of a crossover in the vicinity of an already formed crossover. A poorly studied aspect of the control is chromatid interference. Such analyses are possible in very few organisms as they require observation of all four products of a single meiosis. Here, we provide direct evidence of chromatid interference. Using in situ probing in two interspecific plant hybrids (Lolium multiflorum×Festuca pratensis and Allium cepa×A. roylei) during anaphase I, we demonstrate that the involvement of four chromatids in double crossovers is significantly more frequent than expected (64% versus 25%). We also provide a physical measure of the crossover interference distance, covering ~30-40% of the relative chromosome arm length, and show that the centromere acts as a barrier for crossover interference. The two arms of a chromosome appear to act as independent units in the process of crossing over. Chromatid interference has to be seriously addressed in genetic mapping approaches and further studies.
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Affiliation(s)
- Marco Tulio Mendes Ferreira
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Department of Biology, Federal University of Lavras, Lavras-MG, Brazil
| | - Marek Glombik
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska, Brno, Czech Republic
| | - Kateřina Perničková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska, Brno, Czech Republic
| | - Martin Duchoslav
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Olga Scholten
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Correspondence:
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Mukaj A, Piálek J, Fotopulosova V, Morgan AP, Odenthal-Hesse L, Parvanov ED, Forejt J. Prdm9 Intersubspecific Interactions in Hybrid Male Sterility of House Mouse. Mol Biol Evol 2020; 37:3423-3438. [PMID: 32642764 PMCID: PMC7743643 DOI: 10.1093/molbev/msaa167] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
The classical definition posits hybrid sterility as a phenomenon when two parental taxa each of which is fertile produce a hybrid that is sterile. The first hybrid sterility gene in vertebrates, Prdm9, coding for a histone methyltransferase, was identified in crosses between two laboratory mouse strains derived from Mus mus musculus and M. m. domesticus subspecies. The unique function of PRDM9 protein in the initiation of meiotic recombination led to the discovery of the basic molecular mechanism of hybrid sterility in laboratory crosses. However, the role of this protein as a component of reproductive barrier outside the laboratory model remained unclear. Here, we show that the Prdm9 allelic incompatibilities represent the primary cause of reduced fertility in intersubspecific hybrids between M. m. musculus and M. m. domesticus including 16 musculus and domesticus wild-derived strains. Disruption of fertility phenotypes correlated with the rate of failure of synapsis between homologous chromosomes in meiosis I and with early meiotic arrest. All phenotypes were restored to normal when the domesticus Prdm9dom2 allele was substituted with the Prdm9dom2H humanized variant. To conclude, our data show for the first time the male infertility of wild-derived musculus and domesticus subspecies F1 hybrids controlled by Prdm9 as the major hybrid sterility gene. The impairment of fertility surrogates, testes weight and sperm count, correlated with increasing difficulties of meiotic synapsis of homologous chromosomes and with meiotic arrest, which we suppose reflect the increasing asymmetry of PRDM9-dependent DNA double-strand breaks.
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Affiliation(s)
- Amisa Mukaj
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jaroslav Piálek
- Research Facility Studenec, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Vladana Fotopulosova
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | | | - Linda Odenthal-Hesse
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Emil D Parvanov
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
| | - Jiri Forejt
- Department of Mouse Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Science, Vestec, Czech Republic
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Global Picture of Genetic Relatedness and the Evolution of Humankind. BIOLOGY 2020; 9:biology9110392. [PMID: 33182715 PMCID: PMC7696950 DOI: 10.3390/biology9110392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022]
Abstract
Simple Summary The intricacies of human ancestry are buried deep within our DNA. For years, scientists have been working to piece together a vast picture of our genetic lineage. The purpose of this study was to further reveal this global picture of human genetic relatedness using identical-by-descent (IBD) genomic fragments. We processed over 65 million very rare single nucleotide polymorphic (SNP) alleles and detected over 17 million shared IBD fragments, including very short IBD fragments that allowed us to trace common ancestors back to 200,000 years ago. We also determined nine geographical regions representing nine unique genetic components for mankind: East and West Africa, Northern Europe, Arctica, East Asia, Oceania, South Asia, Middle East, and South America. The levels of admixture in every studied population could be assigned to one of these regions and long-term neighboring populations are strikingly similar, despite any political, religious, and cultural differences. Additionally, we observed the topmost admixture to be in central Eurasia. The entire picture of relatedness of all the studied populations presents itself in the form of shared number/size of IBDs, providing novel insights into geographical admixtures and genetic contributions that shaped human ancestry into what it is today. Abstract We performed an exhaustive pairwise comparison of whole-genome sequences of 3120 individuals, representing 232 populations from all continents and seven prehistoric people including archaic and modern humans. In order to reveal an intricate picture of worldwide human genetic relatedness, 65 million very rare single nucleotide polymorphic (SNP) alleles have been bioinformatically processed. The number and size of shared identical-by-descent (IBD) genomic fragments for every pair of 3127 individuals have been revealed. Over 17 million shared IBD fragments have been described. Our approach allowed detection of very short IBD fragments (<20 kb) that trace common ancestors who lived up to 200,000 years ago. We detected nine distinct geographical regions within which individuals had strong genetic relatedness, but with negligible relatedness between the populations of these regions. The regions, comprising nine unique genetic components for mankind, are the following: East and West Africa, Northern Europe, Arctica, East Asia, Oceania, South Asia, Middle East, and South America. The level of admixture in every studied population has been apportioned among these nine genetic components. Genetically, long-term neighboring populations are strikingly similar to each other in spite of any political, religious, and cultural differences. The topmost admixture has been observed at the center of Eurasia. These admixed populations (including Uyghurs, Azerbaijanis, Uzbeks, and Iranians) have roughly equal genetic contributions from the Middle East, Europe, China, and India, with additional significant traces from Africa and Arctic. The entire picture of relatedness of all the studied populations unfolds and presents itself in the form of shared number/size of IBDs.
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