1
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McAllester CS, Pool JE. Inversions Can Accumulate Balanced Sexual Antagonism: Evidence from Simulations and Drosophila Experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.02.560529. [PMID: 37873205 PMCID: PMC10592935 DOI: 10.1101/2023.10.02.560529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Chromosomal inversion polymorphisms can be common, but the causes of their persistence are often unclear. We propose a model for the maintenance of inversion polymorphism, which requires that some variants contribute antagonistically to two phenotypes, one of which has negative frequency-dependent fitness. These conditions yield a form of frequency-dependent disruptive selection, favoring two predominant haplotypes segregating alleles that favor opposing antagonistic phenotypes. An inversion associated with one haplotype can reduce the fitness load incurred by generating recombinant offspring, reinforcing its linkage to the haplotype and enabling both haplotypes to accumulate more antagonistic variants than expected otherwise. We develop and apply a forward simulator to examine these dynamics under a tradeoff between survival and male display. These simulations indeed generate inversion-associated haplotypes with opposing sex-specific fitness effects. Antagonism strengthens with time, and can ultimately yield karyotypes at surprisingly predictable frequencies, with striking genotype frequency differences between sexes and between developmental stages. To test whether this model may contribute to well-studied yet enigmatic inversion polymorphisms in Drosophila melanogaster, we track inversion frequencies in laboratory crosses to test whether they influence male reproductive success or survival. We find that two of the four tested inversions show significant evidence for the tradeoff examined, with In(3R)K favoring survival and In(3L)Ok favoring male reproduction. In line with the apparent sex-specific fitness effects implied for both of those inversions, In(3L)Ok was also found to be less costly to the viability and/or longevity of males than females, whereas In(3R)K was more beneficial to female survival. Based on this work, we expect that balancing selection on antagonistically pleiotropic traits may provide a significant and underappreciated contribution to the maintenance of natural inversion polymorphism.
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Affiliation(s)
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin – Madison, USA
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2
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Brady MJ, Cheam M, Gent JI, Dawe RK. The maize striate leaves2 ( sr2) gene encodes a conserved DUF3732 domain and is homologous to the rice yss1 gene. PLANT DIRECT 2024; 8:e567. [PMID: 38357415 PMCID: PMC10864124 DOI: 10.1002/pld3.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Maize striate leaves2 (sr2) is a mutant that causes white stripes on leaves that has been used in mapping studies for decades though the underlying gene has not been identified. The sr2 locus has been previously mapped to small regions of normal chromosome 10 (N10) and a rearranged variant called abnormal chromosome 10 (Ab10). A comparison of assembled genomes carrying N10 and Ab10 revealed only five candidate sr2 genes. Analysis of a stock carrying the sr2 reference allele (sr2-ref) showed that one of the five genes has a transposon insertion that disrupts its protein sequence and has a severe reduction in mRNA. An independent Mutator transposon insertion in the gene (sr2-Mu) failed to complement the sr2-ref mutation, and plants homozygous for sr2-Mu showed white striped leaf margins. The sr2 gene encodes a DUF3732 protein with strong homology to a rice gene with a similar mutant phenotype called young seedling stripe1 (yss1). These and other published data suggest that sr2 may have a function in plastid gene expression.
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Affiliation(s)
| | - Maya Cheam
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Jonathan I. Gent
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - R. Kelly Dawe
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
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3
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Finseth F. Female meiotic drive in plants: mechanisms and dynamics. Curr Opin Genet Dev 2023; 82:102101. [PMID: 37633231 DOI: 10.1016/j.gde.2023.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/10/2023] [Accepted: 07/22/2023] [Indexed: 08/28/2023]
Abstract
Female meiosis is fundamentally asymmetric, creating an arena for genetic elements to compete for inclusion in the egg to maximize their transmission. Centromeres, as mediators of chromosomal segregation, are prime candidates to evolve via 'female meiotic drive'. According to the centromere-drive model, the asymmetry of female meiosis ignites a coevolutionary arms race between selfish centromeres and kinetochore proteins, the by-product of which is accelerated sequence divergence. Here, I describe and compare plant models that have been instrumental in uncovering the mechanistic basis of female meiotic drive (maize) and the dynamics of active selfish centromeres in nature (monkeyflowers). Then, I speculate on the mechanistic basis of drive in monkeyflowers, discuss how centromere strength influences chromosomal segregation in plants, and describe new insights into the evolution of plant centromeres.
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Affiliation(s)
- Findley Finseth
- W.M. Keck Science Department, Claremont McKenna, Scripps, and Pitzer Colleges, Claremont, CA 91711, USA.
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4
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The maize abnormal chromosome 10 meiotic drive haplotype: a review. Chromosome Res 2022; 30:205-216. [PMID: 35652970 DOI: 10.1007/s10577-022-09693-6] [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: 02/08/2022] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022]
Abstract
The maize abnormal chromosome 10 (Ab10) haplotype encodes a meiotic drive system that converts heterochromatic knobs into centromere-like bodies that are preferentially segregated through female meiosis. Ab10 was first described in the 1940s and has been intensively studied. Here I provide a comprehensive review of the literature, starting from the discovery of knobs and Ab10, preceding through the classic literature, and finishing with molecular structure and mechanisms. The defining features of the Ab10 haplotype are its two specialized kinesins, Kinesin driver and TR-1 kinesin, that activate neocentromeres at knobs containing different classes of the tandem repeat. In most Ab10 haplotypes, the two kinesin/knob systems cooperate to promote maximum meiotic drive. However, recent interpretations suggest that each kinesin/knob system can function as an independent meiotic driver and that in some cases they compete with each other. Ab10 is present at low frequencies throughout the genus Zea and has significantly expanded genome size by promoting the formation of knobs throughout the genome.
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5
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Song B, Marco-Sola S, Moreto M, Johnson L, Buckler ES, Stitzer MC. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. Proc Natl Acad Sci U S A 2022; 119:e2113075119. [PMID: 34934012 PMCID: PMC8740769 DOI: 10.1073/pnas.2113075119] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/04/2022] Open
Abstract
Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment strategies often produce limited or incongruous results when applied to genomes with dispersed repeats, long indels, and highly diverse sequences. Moreover, alignment using many-to-many or reciprocal best hit approaches conflicts with well-studied patterns between species with different rounds of whole-genome duplication. Here, we introduce Anchored Wavefront alignment (AnchorWave), which performs whole-genome duplication-informed collinear anchor identification between genomes and performs base pair-resolved global alignment for collinear blocks using a two-piece affine gap cost strategy. This strategy enables AnchorWave to precisely identify multikilobase indels generated by transposable element (TE) presence/absence variants (PAVs). When aligning two maize genomes, AnchorWave successfully recalled 87% of previously reported TE PAVs. By contrast, other genome alignment tools showed low power for TE PAV recall. AnchorWave precisely aligns up to three times more of the genome as position matches or indels than the closest competitive approach when comparing diverse genomes. Moreover, AnchorWave recalls transcription factor-binding sites at a rate of 1.05- to 74.85-fold higher than other tools with significantly lower false-positive alignments. AnchorWave complements available genome alignment tools by showing obvious improvement when applied to genomes with dispersed repeats, active TEs, high sequence diversity, and whole-genome duplication variation.
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Affiliation(s)
- Baoxing Song
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
| | - Santiago Marco-Sola
- Department of Computer Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
- Departament d'Arquitectura de Computadors i Sistemes Operatius, Universitat Autònoma de Barcelona, Barcelona 08193, Spain
| | - Miquel Moreto
- Department of Computer Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
- Departament d'Arquitectura de Computadors, Universitat Politècnica de Catalunya, Barcelona 08034, Spain
| | - Lynn Johnson
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- Agricultural Research Service, US Department of Agriculture, Ithaca, NY 14853
| | - Michelle C Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853;
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
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6
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Song B, Buckler ES, Wang H, Wu Y, Rees E, Kellogg EA, Gates DJ, Khaipho-Burch M, Bradbury PJ, Ross-Ibarra J, Hufford MB, Romay MC. Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize. Genome Res 2021; 31:1245-1257. [PMID: 34045362 PMCID: PMC8256870 DOI: 10.1101/gr.266528.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/21/2021] [Indexed: 01/16/2023]
Abstract
Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. More than half of putative cis-regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.
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Affiliation(s)
- Baoxing Song
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA
| | - Hai Wang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yaoyao Wu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Evan Rees
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | | | - Daniel J Gates
- Department of Evolution and Ecology, University of California Davis, Davis, California 95616, USA
| | - Merritt Khaipho-Burch
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Peter J Bradbury
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California Davis, Davis, California 95616, USA
- Center for Population Biology and Genome Center, University of California Davis, Davis, California 95616, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
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7
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Swentowsky KW, Gent JI, Lowry EG, Schubert V, Ran X, Tseng KF, Harkess AE, Qiu W, Dawe RK. Distinct kinesin motors drive two types of maize neocentromeres. Genes Dev 2020; 34:1239-1251. [PMID: 32820038 PMCID: PMC7462060 DOI: 10.1101/gad.340679.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022]
Abstract
A maize chromosome variant called abnormal chromosome 10 (Ab10) converts knobs on chromosome arms into neocentromeres, causing their preferential segregation to egg cells in a process known as meiotic drive. We previously demonstrated that the gene Kinesin driver (Kindr) on Ab10 encodes a kinesin-14 required to mobilize neocentromeres made up of the major tandem repeat knob180. Here we describe a second kinesin-14 gene, TR-1 kinesin (Trkin), that is required to mobilize neocentromeres made up of the minor tandem repeat TR-1. Trkin lies in a 4-Mb region of Ab10 that is not syntenic with any other region of the maize genome and shows extraordinary sequence divergence from Kindr and other kinesins in plants. Despite its unusual structure, Trkin encodes a functional minus end-directed kinesin that specifically colocalizes with TR-1 in meiosis, forming long drawn out neocentromeres. TRKIN contains a nuclear localization signal and localizes to knobs earlier in prophase than KINDR. The fact that TR-1 repeats often co-occur with knob180 repeats suggests that the current role of the TRKIN/TR-1 system is to facilitate the meiotic drive of the KINDR/knob180 system.
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Affiliation(s)
- Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Elizabeth G Lowry
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Veit Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466 Seeland, Germany
| | - Xia Ran
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Kuo-Fu Tseng
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - Alex E Harkess
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA
| | - Weihong Qiu
- Department of Physics, Oregon State University, Corvallis, Oregon 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens Georgia 30602, USA.,Department of Genetics, University of Georgia, Athens Georgia 30602, USA
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8
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Liu J, Seetharam AS, Chougule K, Ou S, Swentowsky KW, Gent JI, Llaca V, Woodhouse MR, Manchanda N, Presting GG, Kudrna DA, Alabady M, Hirsch CN, Fengler KA, Ware D, Michael TP, Hufford MB, Dawe RK. Gapless assembly of maize chromosomes using long-read technologies. Genome Biol 2020; 21:121. [PMID: 32434565 PMCID: PMC7238635 DOI: 10.1186/s13059-020-02029-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Victor Llaca
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | | | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gernot G Presting
- Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Magdy Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Georgia Genomics and Bioinformatics Core Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Kevin A Fengler
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, 14853, USA
| | - Todd P Michael
- Informatics Department, J. Craig Venter Institute, La Jolla, CA, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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9
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Liu J, Seetharam AS, Chougule K, Ou S, Swentowsky KW, Gent JI, Llaca V, Woodhouse MR, Manchanda N, Presting GG, Kudrna DA, Alabady M, Hirsch CN, Fengler KA, Ware D, Michael TP, Hufford MB, Dawe RK. Gapless assembly of maize chromosomes using long-read technologies. Genome Biol 2020. [PMID: 32434565 DOI: 10.1101/2020.01.14.906230v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Victor Llaca
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | | | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gernot G Presting
- Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Magdy Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Georgia Genomics and Bioinformatics Core Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Kevin A Fengler
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, 14853, USA
| | - Todd P Michael
- Informatics Department, J. Craig Venter Institute, La Jolla, CA, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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10
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Roessler K, Muyle A, Diez CM, Gaut GRJ, Bousios A, Stitzer MC, Seymour DK, Doebley JF, Liu Q, Gaut BS. The genome-wide dynamics of purging during selfing in maize. NATURE PLANTS 2019; 5:980-990. [PMID: 31477888 DOI: 10.1038/s41477-019-0508-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 07/26/2019] [Indexed: 05/07/2023]
Abstract
Self-fertilization (also known as selfing) is an important reproductive strategy in plants and a widely applied tool for plant genetics and plant breeding. Selfing can lead to inbreeding depression by uncovering recessive deleterious variants, unless these variants are purged by selection. Here we investigated the dynamics of purging in a set of eleven maize lines that were selfed for six generations. We show that heterozygous, putatively deleterious single nucleotide polymorphisms are preferentially lost from the genome during selfing. Deleterious single nucleotide polymorphisms were lost more rapidly in regions of high recombination, presumably because recombination increases the efficacy of selection by uncoupling linked variants. Overall, heterozygosity decreased more slowly than expected, by an estimated 35% to 40% per generation instead of the expected 50%, perhaps reflecting pervasive associative overdominance. Finally, three lines exhibited marked decreases in genome size due to the purging of transposable elements. Genome loss was more likely to occur for lineages that began with larger genomes with more transposable elements and chromosomal knobs. These three lines purged an average of 398 Mb from their genomes, an amount equivalent to three Arabidopsis thaliana genomes per lineage, in only a few generations.
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Affiliation(s)
- Kyria Roessler
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | | | | | | | | | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, WI, USA
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zheijang Province, College of Agriculture and Food Sciences, Zhejiang A&F University, Lin'an, Hangzhou, China.
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, USA.
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11
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Habig M, Kema GHJ, Holtgrewe Stukenbrock E. Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus. eLife 2018; 7:e40251. [PMID: 30543518 PMCID: PMC6331196 DOI: 10.7554/elife.40251] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/13/2018] [Indexed: 01/03/2023] Open
Abstract
Meiosis is a key cellular process of sexual reproduction that includes pairing of homologous sequences. In many species however, meiosis can also involve the segregation of supernumerary chromosomes, which can lack a homolog. How these unpaired chromosomes undergo meiosis is largely unknown. In this study we investigated chromosome segregation during meiosis in the haploid fungus Zymoseptoria tritici that possesses a large complement of supernumerary chromosomes. We used isogenic whole chromosome deletion strains to compare meiotic transmission of chromosomes when paired and unpaired. Unpaired chromosomes inherited from the male parent as well as paired supernumerary chromosomes in general showed Mendelian inheritance. In contrast, unpaired chromosomes inherited from the female parent showed non-Mendelian inheritance but were amplified and transmitted to all meiotic products. We concluded that the supernumerary chromosomes of Z. tritici show a meiotic drive and propose an additional feedback mechanism during meiosis, which initiates amplification of unpaired female-inherited chromosomes.
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Affiliation(s)
- Michael Habig
- Environmental GenomicsChristian-Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Gert HJ Kema
- Wageningen Plant ResearchWageningen University and ResearchWageningenThe Netherlands
- Laboratory of PhytopathologyWageningen University and ResearchWageningenThe Netherlands
| | - Eva Holtgrewe Stukenbrock
- Environmental GenomicsChristian-Albrechts University of KielKielGermany
- Max Planck Institute for Evolutionary BiologyPlönGermany
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12
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A Kinesin-14 Motor Activates Neocentromeres to Promote Meiotic Drive in Maize. Cell 2018; 173:839-850.e18. [DOI: 10.1016/j.cell.2018.03.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 01/08/2023]
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13
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Abstract
Autosomal drivers violate Mendel’s law of segregation in that they are overrepresented in gametes of heterozygous parents. For drivers to be polymorphic within populations rather than fixing, their transmission advantage must be offset by deleterious effects on other fitness components. In this paper, we develop an analytical model for the evolution of autosomal drivers that is motivated by the neocentromere drive system found in maize. In particular, we model both the transmission advantage and deleterious fitness effects on seed viability, pollen viability, seed to adult survival mediated by maternal genotype, and seed to adult survival mediated by offspring genotype. We derive general, biologically intuitive conditions for the four most likely evolutionary outcomes and discuss the expected evolution of autosomal drivers given these conditions. Finally, we determine the expected equilibrium allele frequencies predicted by the model given recent estimates of fitness components for all relevant genotypes and show that the predicted equilibrium is within the range observed in maize land races for levels of drive at the low end of what has been observed.
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Fitness Costs and Variation in Transmission Distortion Associated with the Abnormal Chromosome 10 Meiotic Drive System in Maize. Genetics 2017; 208:297-305. [PMID: 29122827 DOI: 10.1534/genetics.117.300060] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023] Open
Abstract
Meiotic drive describes a process whereby selfish genetic elements are transmitted at levels greater than Mendelian expectations. Maize abnormal chromosome 10 (Ab10) encodes a meiotic drive system that exhibits strong preferential segregation through female gametes. We performed transmission assays on nine Ab10 chromosomes from landraces and teosinte lines and found a transmission advantage of 62-79% in heterozygotes. Despite this transmission advantage, Ab10 is present at low frequencies in natural populations, suggesting that it carries large negative fitness consequences. We measured pollen transmission, the percentage of live pollen, seed production, and seed size to estimate several of the possible fitness effects of Ab10. We found no evidence that Ab10 affects pollen transmission, i.e., Ab10 and N10 pollen are transmitted equally from heterozygous fathers. However, at the diploid (sporophyte) level, both heterozygous and homozygous Ab10-I-MMR individuals show decreased pollen viability, decreased seed set, and decreased seed weight. The observed fitness costs can nearly but not entirely account for the observed frequencies of Ab10. Sequence analysis shows a surprising amount of molecular variation among Ab10 haplotypes, suggesting that there may be other phenotypic variables that contribute to the low but stable equilibrium frequencies.
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15
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16
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Houben A, Banaei-Moghaddam AM, Klemme S, Timmis JN. Evolution and biology of supernumerary B chromosomes. Cell Mol Life Sci 2014; 71:467-78. [PMID: 23912901 PMCID: PMC11113615 DOI: 10.1007/s00018-013-1437-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/02/2013] [Accepted: 07/24/2013] [Indexed: 12/23/2022]
Abstract
B chromosomes (Bs) are dispensable components of the genome exhibiting non-Mendelian inheritance and have been widely reported on over several thousand eukaryotes, but still remain an evolutionary mystery ever since their first discovery over a century ago [1]. Recent advances in genome analysis have significantly improved our knowledge on the origin and composition of Bs in the last few years. In contrast to the prevalent view that Bs do not harbor genes, recent analysis revealed that Bs of sequenced species are rich in gene-derived sequences. We summarize the latest findings on supernumerary chromosomes with a special focus on the origin, DNA composition, and the non-Mendelian accumulation mechanism of Bs.
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Affiliation(s)
- Andreas Houben
- Chromosome Structure and Function Laboratory, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany,
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17
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Abstract
Examples of meiotic drive, the non-Mendelian segregation of a specific genomic region, have been identified in several eukaryotic species. Maize contains the abnormal chromosome 10 (Ab10) drive system that transforms typically inert heterochromatic knobs into centromere-like domains (neocentromeres) that move rapidly poleward along the spindle during meiosis. Knobs can be made of two different tandem repeat sequences (TR-1 and 180-bp repeat), and both repeats have become widespread in Zea species. Here we describe detailed studies of a large knob on chromosome 10 called K10L2. We show that the knob is composed entirely of the TR-1 repeat and is linked to a strong activator of TR-1 neocentromere activity. K10L2 shows weak meiotic drive when paired with N10 but significantly reduces the meiotic drive exhibited by Ab10 (types I or II) in Ab10/K10L2 heterozygotes. These and other data confirm that (1) there are two separate and independent neocentromere activities in maize, (2) that both the TR-1 and knob 180 repeats exhibit meiotic drive (in the presence of other drive genes), and (3) that the two repeats can operate in competition with each other. Our results support the general concept that tandem repeat arrays can engage in arms-race-like struggles and proliferate as an outcome.
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Kanizay LB, Pyhäjärvi T, Lowry EG, Hufford MB, Peterson DG, Ross-Ibarra J, Dawe RK. Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays. Heredity (Edinb) 2013; 110:570-7. [PMID: 23443059 DOI: 10.1038/hdy.2013.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Maize Abnormal chromosome 10 (Ab10) contains a classic meiotic drive system that exploits the asymmetry of meiosis to preferentially transmit itself and other chromosomes containing specialized heterochromatic regions called knobs. The structure and diversity of the Ab10 meiotic drive haplotype is poorly understood. We developed a bacterial artificial chromosome (BAC) library from an Ab10 line and used the data to develop sequence-based markers, focusing on the proximal portion of the haplotype that shows partial homology to normal chromosome 10. These molecular and additional cytological data demonstrate that two previously identified Ab10 variants (Ab10-I and Ab10-II) share a common origin. Dominant PCR markers were used with fluorescence in situ hybridization to assay 160 diverse teosinte and maize landrace populations from across the Americas, resulting in the identification of a previously unknown but prevalent form of Ab10 (Ab10-III). We find that Ab10 occurs in at least 75% of teosinte populations at a mean frequency of 15%. Ab10 was also found in 13% of the maize landraces, but does not appear to be fixed in any wild or cultivated population. Quantitative analyses suggest that the abundance and distribution of Ab10 is governed by a complex combination of intrinsic fitness effects as well as extrinsic environmental variability.
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Affiliation(s)
- L B Kanizay
- Department of Plant Biology, University of Georgia, Athens, GA, USA
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19
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Abstract
Neocentromeres are ectopic sites where new functional kinetochores assemble and permit chromosome segregation. Neocentromeres usually form following genomic alterations that remove or disrupt centromere function. The ability to form neocentromeres is conserved in eukaryotes ranging from fungi to mammals. Neocentromeres that rescue chromosome fragments in cells with gross chromosomal rearrangements are found in several types of human cancers, and in patients with developmental disabilities. In this review, we discuss the importance of neocentromeres to human health and evaluate recently developed model systems to study neocentromere formation, maintenance, and function in chromosome segregation. Additionally, studies of neocentromeres provide insight into native centromeres; analysis of neocentromeres found in human clinical samples and induced in model organisms distinguishes features of centromeres that are dependent on centromere DNA from features that are epigenetically inherited together with the formation of a functional kinetochore.
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20
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Banaei-Moghaddam AM, Schubert V, Kumke K, Weiβ O, Klemme S, Nagaki K, Macas J, González-Sánchez M, Heredia V, Gómez-Revilla D, González-García M, Vega JM, Puertas MJ, Houben A. Nondisjunction in favor of a chromosome: the mechanism of rye B chromosome drive during pollen mitosis. THE PLANT CELL 2012; 24:4124-34. [PMID: 23104833 PMCID: PMC3517240 DOI: 10.1105/tpc.112.105270] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 09/17/2012] [Accepted: 09/30/2012] [Indexed: 05/18/2023]
Abstract
B chromosomes (Bs) are supernumerary components of the genome and do not confer any advantages on the organisms that harbor them. The maintenance of Bs in natural populations is possible by their transmission at higher than Mendelian frequencies. Although drive is the key for understanding B chromosomes, the mechanism is largely unknown. We provide direct insights into the cellular mechanism of B chromosome drive in the male gametophyte of rye (Secale cereale). We found that nondisjunction of Bs is accompanied by centromere activity and is likely caused by extended cohesion of the B sister chromatids. The B centromere originated from an A centromere, which accumulated B-specific repeats and rearrangements. Because of unequal spindle formation at the first pollen mitosis, nondisjoined B chromatids preferentially become located toward the generative pole. The failure to resolve pericentromeric cohesion is under the control of the B-specific nondisjunction control region. Hence, a combination of nondisjunction and unequal spindle formation at first pollen mitosis results in the accumulation of Bs in the generative nucleus and therefore ensures their transmission at a higher than expected rate to the next generation.
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Affiliation(s)
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Oda Weiβ
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Sonja Klemme
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Jiří Macas
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, Ceske Budejovice 37005, Czech Republic
| | - Mónica González-Sánchez
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Victoria Heredia
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Diana Gómez-Revilla
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Miriam González-García
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Juan M. Vega
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Maria J. Puertas
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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21
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Burrack LS, Berman J. Flexibility of centromere and kinetochore structures. Trends Genet 2012; 28:204-12. [PMID: 22445183 DOI: 10.1016/j.tig.2012.02.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 02/13/2012] [Accepted: 02/15/2012] [Indexed: 12/14/2022]
Abstract
Centromeres, and the kinetochores that assemble on them, are essential for accurate chromosome segregation. Diverse centromere organization patterns and kinetochore structures have evolved in eukaryotes ranging from yeast to humans. In addition, centromere DNA and kinetochore position can vary even within individual cells. This flexibility is manifested in several ways: centromere DNA sequences evolve rapidly, kinetochore positions shift in response to altered chromosome structure, and kinetochore complex numbers change in response to fluctuations in kinetochore protein levels. Despite their differences, all of these diverse structures promote efficient chromosome segregation. This robustness is inherent to chromosome segregation mechanisms and balances genome stability with adaptability. In this review, we explore the mechanisms and consequences of centromere and kinetochore flexibility as well as the benefits and limitations of different experimental model systems for their study.
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Affiliation(s)
- Laura S Burrack
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55405, USA
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Kanizay L, Dawe RK. Centromeres: long intergenic spaces with adaptive features. Funct Integr Genomics 2009; 9:287-92. [DOI: 10.1007/s10142-009-0124-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/20/2009] [Accepted: 04/24/2009] [Indexed: 12/12/2022]
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Panchenko T, Black BE. The epigenetic basis for centromere identity. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 48:1-32. [PMID: 19521810 DOI: 10.1007/978-3-642-00182-6_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The centromere serves as the control locus for chromosome segregation at mitosis and meiosis. In most eukaryotes, including mammals, the location of the centromere is epigenetically defined. The contribution of both genetic and epigenetic determinants to centromere function is the subject of current investigation in diverse eukaryotes. Here we highlight key findings from several organisms that have shaped the current view of centromeres, with special attention to experiments that have elucidated the epigenetic nature of their specification. Recent insights into the histone H3 variant, CENP-A, which assembles into centromeric nucleosomes that serve as the epigenetic mark to perpetuate centromere identity, have added important mechanistic understanding of how centromere identity is initially established and subsequently maintained in every cell cycle.
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Affiliation(s)
- Tanya Panchenko
- Department of Biochemistry, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
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24
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Fishman L, Saunders A. Centromere-associated female meiotic drive entails male fitness costs in monkeyflowers. Science 2008; 322:1559-62. [PMID: 19056989 DOI: 10.1126/science.1161406] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Female meiotic drive, in which paired chromosomes compete for access to the egg, is a potentially powerful but rarely documented evolutionary force. In interspecific monkeyflower (Mimulus) hybrids, a driving M. guttatus allele (D) exhibits a 98:2 transmission advantage via female meiosis. We show that extreme interspecific drive is most likely caused by divergence in centromere-associated repeat domains and document cytogenetic and functional polymorphism for drive within a population of M. guttatus. In conspecific crosses, D had a 58:42 transmission advantage over nondriving alternative alleles. However, individuals homozygous for the driving allele suffered reduced pollen viability. These fitness effects and molecular population genetic data suggest that balancing selection prevents the fixation or loss of D and that selfish chromosomal transmission may affect both individual fitness and population genetic load.
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Affiliation(s)
- Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
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Martin N, Ruedi EA, LeDuc R, Sun FJ, Caetano-Anollés G. Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event? Biol Direct 2007; 2:23. [PMID: 17894859 PMCID: PMC2134927 DOI: 10.1186/1745-6150-2-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 09/25/2007] [Indexed: 11/24/2022] Open
Abstract
Background Recent comparative genomic studies claim local syntenic gene-interleaving relationships in Ashbya gossypii and Kluyveromyces waltii are compelling evidence for an ancient whole-genome duplication event in Saccharomyces cerevisiae. We here test, using Hannenhalli-Pevzner rearrangement algorithms that address the multiple genome rearrangement problem, whether syntenic patterns are proof of paleopolyploidization. Results We focus on (1) pairwise comparison of gene arrangement sequences in A. gossypii and S. cerevisiae, (2) reconstruction of gene arrangements ancestral to A. gossypii, S. cerevisiae, and K. waltii, (3) synteny patterns arising within and between lineages, and (4) expected gene orientation of duplicate gene sets. The existence of syntenic patterns between ancestral gene sets and A. gossypii, S. cerevisiae, and K. waltii, and other evidence, suggests that gene-interleaving relationships are the natural consequence of topological rearrangements in chromosomes and that a more gradual scenario of genome evolution involving segmental duplication and recombination constitutes a more parsimonious explanation. Furthermore, phylogenetic trees reconstructed under alternative hypotheses placed the putative whole-genome duplication event after the divergence of the S. cerevisiae and K. waltii lineages, but in the lineage leading to K. waltii. This is clearly incompatible with an ancient genome duplication event in S. cerevisiae. Conclusion Because the presence of syntenic patterns appears to be a condition that is necessary, but not sufficient, to support the existence of the whole-genome duplication event, our results prompt careful re-evaluation of paleopolyploidization in the yeast lineage and the evolutionary meaning of syntenic patterns. Reviewers This article was reviewed by Kenneth H. Wolfe (nominated by Nicolas Galtier), Austin L. Hughes (nominated by Eugene Koonin), Mikhail S. Gelfand, and Mark Gerstein.
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Affiliation(s)
- Nicolas Martin
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Elizabeth A Ruedi
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Richard LeDuc
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Feng-Jie Sun
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 W Peabody Drive, Urbana, IL 61801, USA
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