51
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Birchler JA, Han F. Barbara McClintock's Unsolved Chromosomal Mysteries: Parallels to Common Rearrangements and Karyotype Evolution. THE PLANT CELL 2018; 30:771-779. [PMID: 29545470 PMCID: PMC5969279 DOI: 10.1105/tpc.17.00989] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/08/2018] [Accepted: 03/15/2018] [Indexed: 05/04/2023]
Abstract
Two obscure studies on chromosomal behavior by Barbara McClintock are revisited in light of subsequent studies and evolutionary genomics of chromosome number reduction. The phenomenon of deficiency recovery in which adjacent genetic markers lost in the zygote reappear in later developmental sectors is discussed in light of de novo centromere formation on chromosomal fragments. Second, McClintock described a small chromosome, which she postulated carried an "X component," that fostered specific types of chromosomal rearrangements mainly involving centromere changes and attachments to the termini of chromosomes. These findings are cast in the context of subsequent studies on centromere misdivision, the tendency of broken fragments to join chromosome ends, and the realization from genomic sequences that nested chromosomal insertion and end-to-end chromosomal fusions are common features of karyotype evolution. Together, these results suggest a synthesis that centromere breaks, inactivation, and de novo formation together with telomeres-acting under some circumstances as double-strand DNA breaks that join with others-is the underlying basis of these chromosomal phenomena.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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52
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Klein SJ, O'Neill RJ. Transposable elements: genome innovation, chromosome diversity, and centromere conflict. Chromosome Res 2018; 26:5-23. [PMID: 29332159 PMCID: PMC5857280 DOI: 10.1007/s10577-017-9569-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022]
Abstract
Although it was nearly 70 years ago when transposable elements (TEs) were first discovered “jumping” from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive. Finally, we focus on the role of TEs in the establishment, maintenance, and stabilization of critical, yet rapidly evolving, chromosome features: eukaryotic centromeres. Across centromeres, specific types of TEs participate in genomic conflict, a balancing act wherein they are actively inserting into centromeric domains yet are harnessed for the recruitment of centromeric histones and potentially new centromere formation.
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Affiliation(s)
- Savannah J Klein
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
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53
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Henikoff S, Thakur J, Kasinathan S, Talbert PB. Remarkable Evolutionary Plasticity of Centromeric Chromatin. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:71-82. [PMID: 29196559 DOI: 10.1101/sqb.2017.82.033605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Centromeres were familiar to cell biologists in the late 19th century, but for most eukaryotes the basis for centromere specification has remained enigmatic. Much attention has been focused on the cenH3 (CENP-A) histone variant, which forms the foundation of the centromere. To investigate the DNA sequence requirements for centromere specification, we applied a variety of epigenomic approaches, which have revealed surprising diversity in centromeric chromatin properties. Whereas each point centromere of budding yeast is occupied by a single precisely positioned tetrameric nucleosome with one cenH3 molecule, the "regional" centromeres of fission yeast contain unphased presumably octameric nucleosomes with two cenH3s. In Caenorhabditis elegans, kinetochores assemble all along the chromosome at sites of cenH3 nucleosomes that resemble budding yeast point centromeres, whereas holocentric insects lack cenH3 entirely. The "satellite" centromeres of most animals and plants consist of cenH3-containing particles that are precisely positioned over homogeneous tandem repeats, but in humans, different α-satellite subfamilies are occupied by CENP-A nucleosomes with very different conformations. We suggest that this extraordinary evolutionary diversity of centromeric chromatin architectures can be understood in terms of the simplicity of the task of equal chromosome segregation that is continually subverted by selfish DNA sequences.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Jitendra Thakur
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Sivakanthan Kasinathan
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109.,Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195
| | - Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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54
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Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize. Proc Natl Acad Sci U S A 2017; 114:12231-12236. [PMID: 29087335 DOI: 10.1073/pnas.1713225114] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination is the most important source of genetic variation in higher eukaryotes. It is initiated by formation of double-strand breaks (DSBs) in chromosomal DNA in early meiotic prophase. The DSBs are subsequently repaired, resulting in crossovers (COs) and noncrossovers (NCOs). Recombination events are not distributed evenly along chromosomes but cluster at recombination hotspots. How specific sites become hotspots is poorly understood. Studies in yeast and mammals linked initiation of meiotic recombination to active chromatin features present upstream from genes, such as absence of nucleosomes and presence of trimethylation of lysine 4 in histone H3 (H3K4me3). Core recombination components are conserved among eukaryotes, but it is unclear whether this conservation results in universal characteristics of recombination landscapes shared by a wide range of species. To address this question, we mapped meiotic DSBs in maize, a higher eukaryote with a large genome that is rich in repetitive DNA. We found DSBs in maize to be frequent in all chromosome regions, including sites lacking COs, such as centromeres and pericentromeric regions. Furthermore, most DSBs are formed in repetitive DNA, predominantly Gypsy retrotransposons, and only one-quarter of DSB hotspots are near genes. Genic and nongenic hotspots differ in several characteristics, and only genic DSBs contribute to crossover formation. Maize hotspots overlap regions of low nucleosome occupancy but show only limited association with H3K4me3 sites. Overall, maize DSB hotspots exhibit distribution patterns and characteristics not reported previously in other species. Understanding recombination patterns in maize will shed light on mechanisms affecting dynamics of the plant genome.
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55
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Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants. Genes (Basel) 2017; 8:genes8100290. [PMID: 29064432 PMCID: PMC5664140 DOI: 10.3390/genes8100290] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 01/18/2023] Open
Abstract
Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.
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56
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Zhao H, Zeng Z, Koo DH, Gill BS, Birchler JA, Jiang J. Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3. Chromosome Res 2017; 25:299-311. [PMID: 28831743 DOI: 10.1007/s10577-017-9564-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 01/01/2023]
Abstract
Centromeres can arise de novo from non-centromeric regions, which are often called "neocentromeres." Neocentromere formation provides the best evidence for the concept that centromere function is not determined by the underlying DNA sequences, but controlled by poorly understood epigenetic mechanisms. Numerous neocentromeres have been reported in several plant and animal species. However, it has been elusive how and why a specific chromosomal region is chosen to be a new centromere during the neocentromere activation events. We report recurrent establishment of neocentromeres in a pericentromeric region of chromosome 3 in maize (Zea mays). This latent region is located in the short arm and is only 2 Mb away from the centromere (Cen3) of chromosome 3. At least three independent neocentromere activation events, which were likely induced by different mechanisms, occurred within this latent region. We mapped the binding domains of CENH3, the centromere-specific H3 histone variant, of the three neocentromeres and analyzed the genomic and epigenomic features associated with Cen3, the de novo centromeres and an inactivated centromere derived from an ancestral chromosome. Our results indicate that lack of genes and transcription and a relatively high level of DNA methylation in this pericentromeric region may provide a favorable chromatin environment for neocentromere activation.
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Affiliation(s)
- Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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57
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Abstract
Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomycescerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies.
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58
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Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D. Improved maize reference genome with single-molecule technologies. Nature 2017; 546:524-527. [PMID: 28605751 DOI: 10.1101/079004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/14/2017] [Indexed: 05/21/2023]
Abstract
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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Affiliation(s)
- Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Paul Peluso
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Jinghua Shi
- BioNano Genomics, San Diego, California 92121, USA
| | | | - Michelle C Stitzer
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, Davis, California 95616, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Xuehong Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Katherine Guill
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri 65211, USA
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Kevin L Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Thomas K Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Michael R May
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Eric Antoniou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Gernot G Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Michael McMullen
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri 65211, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, Center for Population Biology, and Genome Center, University of California, Davis, California 95616, USA
| | - R Kelly Dawe
- University of Georgia, Athens, Georgia 30602, USA
| | - Alex Hastie
- BioNano Genomics, San Diego, California 92121, USA
| | - David R Rank
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- USDA-ARS, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853, USA
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59
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Gent JI, Wang N, Dawe RK. Stable centromere positioning in diverse sequence contexts of complex and satellite centromeres of maize and wild relatives. Genome Biol 2017. [PMID: 28637491 PMCID: PMC5480163 DOI: 10.1186/s13059-017-1249-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere positioning because many of its large (~2 Mb) centromeres are not dominated by satellite DNA. These centromeres, which we call complex centromeres, allow for both assembly into reference genomes and for mapping short reads from ChIP-seq with antibodies to centromeric histone H3 (cenH3). Results We found frequent complex centromeres in maize and its wild relatives Z. mays parviglumis, Z. mays mexicana, and particularly Z. mays huehuetenangensis. Analysis of individual plants reveals minor variation in the positions of complex centromeres among siblings. However, such positional shifts are stochastic and not heritable, consistent with prior findings that centromere positioning is stable at the population level. Centromeres are also stable in multiple F1 hybrid contexts. Analysis of repeats in Z. mays and other species (Zea diploperennis, Zea luxurians, and Tripsacum dactyloides) reveals tenfold differences in abundance of the major satellite CentC, but similar high levels of sequence polymorphism in individual CentC copies. Deviation from the CentC consensus has little or no effect on binding of cenH3. Conclusions These data indicate that complex centromeres are neither a peculiarity of cultivation nor inbreeding in Z. mays. While extensive arrays of CentC may be the norm for other Zea and Tripsacum species, these data also reveal that a wide diversity of DNA sequences and multiple types of genetic elements in and near centromeres support centromere function and constrain centromere positions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1249-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, USA
| | - R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, USA. .,Department of Genetics, University of Georgia, Athens, USA.
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60
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Improved maize reference genome with single-molecule technologies. Nature 2017; 546:524-527. [PMID: 28605751 PMCID: PMC7052699 DOI: 10.1038/nature22971] [Citation(s) in RCA: 701] [Impact Index Per Article: 100.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/14/2017] [Indexed: 01/01/2023]
Abstract
An improved reference genome for maize, using single-molecule sequencing and high-resolution optical mapping, enables characterization of structural variation and repetitive regions, and identifies lineage expansions of transposable elements that are unique to maize. The maize genome was initially reported in 2009 but with some accuracy limitations. Doreen Ware and colleagues report a new reference genome for maize using single-molecule sequencing and high-resolution optical mapping. The technique shows improvements in the gene space including resolution of gaps and misassemblies and correction of order and orientation of genes. The authors characterize structural variation and repetitive regions, and identify transposable element lineage expansions unique to maize. Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation1. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions2. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome3, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing4. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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61
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Comai L, Maheshwari S, Marimuthu MPA. Plant centromeres. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:158-167. [PMID: 28411416 DOI: 10.1016/j.pbi.2017.03.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 05/24/2023]
Abstract
Plant centromeres, which are determined epigenetically by centromeric histone 3 (CENH3) have revealed surprising structural diversity, ranging from the canonical monocentric seen in vertebrates, to polycentric, and holocentric. Normally stable, centromeres can change position over evolutionary times or upon genomic stress, such as when chromosomes are broken. At the DNA level, centromeres can be based on single copy DNA or more commonly on repeats. Rapid evolution of centromeric sequences and of CENH3 protein remains a mystery, as evidence of co-adaptation is lacking. Epigenetic differences between parents can trigger uniparental centromere failure and genome elimination, contributing to postzygotic hybridization barriers..
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Affiliation(s)
- Luca Comai
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA.
| | - Shamoni Maheshwari
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Mohan P A Marimuthu
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
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62
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Maheshwari S, Ishii T, Brown CT, Houben A, Comai L. Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence. Genome Res 2017; 27:471-478. [PMID: 28223399 PMCID: PMC5340974 DOI: 10.1101/gr.214619.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022]
Abstract
During cell division, spindle fibers attach to chromosomes at centromeres. The DNA sequence at regional centromeres is fast evolving with no conserved genetic signature for centromere identity. Instead CENH3, a centromere-specific histone H3 variant, is the epigenetic signature that specifies centromere location across both plant and animal kingdoms. Paradoxically, CENH3 is also adaptively evolving. An ongoing question is whether CENH3 evolution is driven by a functional relationship with the underlying DNA sequence. Here, we demonstrate that despite extensive protein sequence divergence, CENH3 histones from distant species assemble centromeres on the same underlying DNA sequence. We first characterized the organization and diversity of centromere repeats in wild-type Arabidopsis thaliana. We show that A. thaliana CENH3-containing nucleosomes exhibit a strong preference for a unique subset of centromeric repeats. These sequences are largely missing from the genome assemblies and represent the youngest and most homogeneous class of repeats. Next, we tested the evolutionary specificity of this interaction in a background in which the native A. thaliana CENH3 is replaced with CENH3s from distant species. Strikingly, we find that CENH3 from Lepidium oleraceum and Zea mays, although specifying epigenetically weaker centromeres that result in genome elimination upon outcrossing, show a binding pattern on A. thaliana centromere repeats that is indistinguishable from the native CENH3. Our results demonstrate positional stability of a highly diverged CENH3 on independently evolved repeats, suggesting that the sequence specificity of centromeres is determined by a mechanism independent of CENH3.
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Affiliation(s)
- Shamoni Maheshwari
- Plant Biology Department and Genome Center, University of California, Davis, California 95616, USA
| | - Takayoshi Ishii
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, California 95616, USA
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany
| | - Luca Comai
- Plant Biology Department and Genome Center, University of California, Davis, California 95616, USA
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63
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Liu S, Zheng J, Migeon P, Ren J, Hu Y, He C, Liu H, Fu J, White FF, Toomajian C, Wang G. Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Sci Rep 2017; 7:42444. [PMID: 28186206 PMCID: PMC5301235 DOI: 10.1038/srep42444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/10/2017] [Indexed: 12/15/2022] Open
Abstract
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Cheng He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Taian 271018, P.R. China.,College of Life Sciences, Shandong Agricultural University, Taian 271018, P.R. China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
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64
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Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum. Sci Rep 2017; 7:41659. [PMID: 28134354 PMCID: PMC5278356 DOI: 10.1038/srep41659] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023] Open
Abstract
Sugarcane (Saccharum hybrids spp.) is the most important sugar crop that accounts for ~75% of the world’s sugar production. Recently, a whole-genome sequencing project was launched on the wild species S. spontaneum. To obtain information on the DNA composition of the repeat-enriched region of the centromere, we conducted a genome-wide analysis of the DNA sequences associated with CenH3 (a mutant of histone H3 located in eukaryote centromeres) using chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. We demonstrate that the centromeres contain mainly SCEN-like single satellite repeat (Ss1) and several Ty3/gypsy retrotransposon-related repeats (Ss166, Ss51, and Ss68). Ss1 dominates in the centromeric regions and spans up to 500 kb. In contrast, the Ty3/gypsy retrotransposon-related repeats are either clustered spanning over a short range, or dispersed in the centromere regions. Interestingly, Ss1 exhibits a chromosome-specific enrichment in the wild species S. spontaneum and S. robustum, but not in the domesticated species S. officinarum and modern sugarcane cultivars. This finding suggests an autopolyploid genome identity of S. spontaneum with a high level of homology among its eight sub-genomes. We also conducted a genome-wide survey of the repetitive DNAs in S. spontaneum following a similarity-based sequence clustering strategy. These results provide insight into the composition of sugarcane genome as well as the genome assembly of S. spontaneum.
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He C, Fu J, Zhang J, Li Y, Zheng J, Zhang H, Yang X, Wang J, Wang G. A Gene-Oriented Haplotype Comparison Reveals Recently Selected Genomic Regions in Temperate and Tropical Maize Germplasm. PLoS One 2017; 12:e0169806. [PMID: 28099470 PMCID: PMC5242465 DOI: 10.1371/journal.pone.0169806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/21/2016] [Indexed: 11/19/2022] Open
Abstract
The extensive genetic variation present in maize (Zea mays) germplasm makes it possible to detect signatures of positive artificial selection that occurred during temperate and tropical maize improvement. Here we report an analysis of 532,815 polymorphisms from a maize association panel consisting of 368 diverse temperate and tropical inbred lines. We developed a gene-oriented approach adapting exonic polymorphisms to identify recently selected alleles by comparing haplotypes across the maize genome. This analysis revealed evidence of selection for more than 1100 genomic regions during recent improvement, and included regulatory genes and key genes with visible mutant phenotypes. We find that selected candidate target genes in temperate maize are enriched in biosynthetic processes, and further examination of these candidates highlights two cases, sucrose flux and oil storage, in which multiple genes in a common pathway can be cooperatively selected. Finally, based on available parallel gene expression data, we hypothesize that some genes were selected for regulatory variations, resulting in altered gene expression.
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Affiliation(s)
- Cheng He
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohong Yang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Jianhua Wang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (GW); (JW)
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (GW); (JW)
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Han J, Masonbrink RE, Shan W, Song F, Zhang J, Yu W, Wang K, Wu Y, Tang H, Wendel JF, Wang K. Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:992-1005. [PMID: 27539015 DOI: 10.1111/tpj.13309] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/07/2016] [Accepted: 08/11/2016] [Indexed: 05/27/2023]
Abstract
Centromeric chromatin in most eukaryotes is composed of highly repetitive centromeric retrotransposons and satellite repeats that are highly variable even among closely related species. The evolutionary mechanisms that underlie the rapid evolution of centromeric repeats remain unknown. To obtain insight into the evolution of centromeric repeats following polyploidy, we studied a model diploid progenitor (Gossypium raimondii, D-genome) of the allopolyploid (AD-genome) cottons, G. hirsutum and G. barbadense. Sequence analysis of chromatin-immunoprecipitated DNA showed that the G. raimondii centromeric repeats originated from retrotransposon-related sequences. Comparative analysis showed that nine of the 10 analyzed centromeric repeats were absent from the centromeres in the A-genome and related diploid species (B-, F- and G-genomes), indicating that they colonized the centromeres of D-genome lineage after the divergence of the A- and D- ancestral species or that they were ancestrally retained prior to the origin of Gossypium. Notably, six of the nine repeats were present in both the A- and D-subgenomes in tetraploid G. hirsutum, and increased in abundance in both subgenomes. This finding suggests that centromeric repeats may spread and proliferate between genomes subsequent to polyploidization. Two repeats, Gr334 and Gr359 occurred in both the centromeres and nucleolar organizer regions (NORs) in D- and AD-genome species, yet localized to just the NORs in A-, B-, F-, and G-genome species. Contained within is a story of an established centromeric repeat that is eliminated and allopolyploidization provides an opportunity for reinvasion and reestablishment, which broadens our evolutionary understanding behind the cycles of centromeric repeat establishment and targeting.
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Affiliation(s)
- Jinlei Han
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Rick E Masonbrink
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Wenbo Shan
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Fengqin Song
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Weichang Yu
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, China
| | - Yufeng Wu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kai Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
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Xiong W, Dooner HK, Du C. Rolling-circle amplification of centromeric Helitrons in plant genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:1038-1045. [PMID: 27553634 DOI: 10.1111/tpj.13314] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The unusual eukaryotic Helitron transposons can readily capture host sequences and are, thus, evolutionarily important. They are presumed to amplify by rolling-circle replication (RCR) because some elements encode predicted proteins homologous to RCR prokaryotic transposases. In support of this replication mechanism, it was recently shown that transposition of a bat Helitron generates covalently closed circular intermediates. Another strong prediction is that RCR should generate tandem Helitron concatemers, yet almost all Helitrons identified to date occur as solo elements in the genome. To investigate alternative modes of Helitron organization in present-day genomes, we have applied the novel computational tool HelitronScanner to 27 plant genomes and have uncovered numerous tandem arrays of partially decayed, truncated Helitrons in all of them. Strikingly, most of these Helitron tandem arrays are interspersed with other repeats in centromeres. Many of these arrays have multiple Helitron 5' ends, but a single 3' end. The number of repeats in any one array can range from a handful to several hundreds. We propose here an RCR model that conforms to the present Helitron landscape of plant genomes. Our study provides strong evidence that plant Helitrons amplify by RCR and that the tandemly arrayed replication products accumulate mostly in centromeres.
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Affiliation(s)
- Wenwei Xiong
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA
| | - Hugo K Dooner
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ, 08801, USA
| | - Chunguang Du
- Department of Biology, Montclair State University, Montclair, NJ, 07043, USA
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Fransz P, Linc G, Lee C, Aflitos SA, Lasky JR, Toomajian C, Ali H, Peters J, van Dam P, Ji X, Kuzak M, Gerats T, Schubert I, Schneeberger K, Colot V, Martienssen R, Koornneef M, Nordborg M, Juenger TE, de Jong H, Schranz ME. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:159-178. [PMID: 27436134 PMCID: PMC5113708 DOI: 10.1111/tpj.13262] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 05/02/2023]
Abstract
Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17-Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F-box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col-FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South-Eastern Europe approximately 5000 years ago and the FRI-Col allele to North-West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The 'American haplotype' was identified from several European localities, potentially due to return migration.
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Affiliation(s)
- Paul Fransz
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
| | - Gabriella Linc
- Department of Plant Development and (Epi)GeneticsSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Centre for Agricultural ResearchHungarian Academy of SciencesAgricultural InstituteMartonvásárHungary
| | - Cheng‐Ruei Lee
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Jesse R. Lasky
- Department of BiologyPennsylvania State UniversityUniversity ParkPAUSA
| | | | - Hoda Ali
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
- Present address: Department of Genetics and CytologyNational Research CenterCairoEgypt
| | - Janny Peters
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Peter van Dam
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
- Present address: Department of Molecular Plant PathologyUniversity of AmsterdamAmsterdamThe Netherlands
| | - Xianwen Ji
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
| | - Mateusz Kuzak
- MAD, Dutch Genomics Service & Support ProviderSwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamthe Netherlands
- Present address: Netherlands eScience CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Tom Gerats
- Section Plant GeneticsInstitute for Wetland and Water Research Faculty of ScienceRadboud UniversityNijmegenthe Netherlands
| | - Ingo Schubert
- Department of Cytogenetics and Genome AnalysisThe Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | | | - Vincent Colot
- Unité de Recherche en Génomique Végétale (URGV)INRA/CNRS/UEVE 2 Rue Gaston CrémieuxEvry Cedex91057France
- Present address: Institut de Biologie de l'Ecole Normale Supérieure (IBENS)ParisFrance
| | - Rob Martienssen
- Cold Spring Harbor LaboratoryCold Spring HarborNew YorkNY11724USA
| | - Maarten Koornneef
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
- Max Planck Institute for Plant Breeding ResearchKöln50829Germany
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna Biocenter (VBC)Dr Bohr‐Gasse 3Vienna1030Austria
| | | | - Hans de Jong
- Laboratory of GeneticsWageningen UniversityWageningenthe Netherlands
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Zedek F, Bureš P. CenH3 evolution reflects meiotic symmetry as predicted by the centromere drive model. Sci Rep 2016; 6:33308. [PMID: 27629066 PMCID: PMC5024113 DOI: 10.1038/srep33308] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/24/2016] [Indexed: 11/09/2022] Open
Abstract
The centromere drive model explaining rapid evolution of eukaryotic centromeres predicts higher frequency of positive selection acting on centromeric histone H3 (CenH3) in clades with asymmetric meiosis compared to the clades with only symmetric meiosis. However, despite the impression one might get from the literature, this key prediction of the centromere drive model has not only never been confirmed, but it has never been tested, because all the previous studies dealt only with the presence or absence instead of the frequency of positive selection. To provide evidence for or against different frequencies of positively selected CenH3 in asymmetrics and symmetrics, we have inferred the selective pressures acting on CenH3 in seventeen eukaryotic clades, including plants, animals, fungi, ciliates and apicomplexa, using codon-substitution models, and compared the inferred frequencies between asymmetrics and symmetrics in a quantitative manner. We have found that CenH3 has been evolving adaptively much more frequently in clades with asymmetric meiosis compared with clades displaying only symmetric meiosis which confirms the prediction of centromere drive model. Our findings indicate that the evolution of asymmetric meiosis required CenH3 to evolve adaptively more often to counterbalance the negative consequences of centromere drive.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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Wolfgruber TK, Nakashima MM, Schneider KL, Sharma A, Xie Z, Albert PS, Xu R, Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting GG. High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events. FRONTIERS IN PLANT SCIENCE 2016; 7:308. [PMID: 27047500 PMCID: PMC4806543 DOI: 10.3389/fpls.2016.00308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/27/2016] [Indexed: 05/02/2023]
Abstract
The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR) has presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here, we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 × 10(-6) and 5 × 10(-5) for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb from the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length CR from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB) repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. In many cases examined here, DSB repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to efficiently repair frequent DSBs in centromeres.
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Affiliation(s)
- Thomas K. Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Megan M. Nakashima
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Kevin L. Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Anupma Sharma
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Zidian Xie
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Patrice S. Albert
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Ronghui Xu
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Paul Bilinski
- Department of Plant Sciences, University of California DavisDavis, CA, USA
| | - R. Kelly Dawe
- Department of Plant Biology, University of GeorgiaAthens, GA, USA
| | | | - James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Gernot G. Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
- *Correspondence: Gernot G. Presting
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