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Characterization of the microsatellite landscape provides insights into the evolutionary dynamics of the mammals based on the chromosome-level genomes. Gene X 2023; 851:146965. [DOI: 10.1016/j.gene.2022.146965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/18/2022] [Accepted: 10/11/2022] [Indexed: 11/27/2022] Open
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Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J. Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays. FRONTIERS IN PLANT SCIENCE 2016; 7:1433. [PMID: 27713757 PMCID: PMC5031598 DOI: 10.3389/fpls.2016.01433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.
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Affiliation(s)
| | | | | | | | - Nathan Garcia
- National Center for Genome Resources, Santa FeNM, USA
| | | | | | | | - Yan He
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Minghui Wang
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Qi Sun
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Jaroslaw Pillardy
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
- *Correspondence: Joann Mudge,
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Marsolier-Kergoat MC. Models for the evolution of GC content in asexual fungi Candida albicans and C. dubliniensis. Genome Biol Evol 2014; 5:2205-16. [PMID: 24179136 PMCID: PMC3845650 DOI: 10.1093/gbe/evt170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Although guanine–cytosine (GC)-biased gene conversion (gBGC) following meiotic recombination seems the most probable mechanism accounting for large-scale variations in GC content for many eukaryotes, it cannot explain such variations for organisms belonging to ancient asexual lineages, such as the pathogenic fungi Candida albicans and C. dubliniensis. Analysis of the substitution patterns for these two species reveals a strong anticorrelation between the synonymous transition rates at third codon positions. I propose two models that can account for this observation. According to the first model, the evolution of GC content is driven by gBGC linked to mitotic recombination, either associated with parasexuality or with damage repair. Variations in the GC content thus reflect variations in the strength of gBGC, presumably variations in the mitotic recombination rate. According to the second model, the evolution of GC content is driven by misincorporation errors during the process of DNA replication in S phase. This model proposes that variations in GC content are due to variations in the proportions of dCTPs and dGTPs at the time when sequences are replicated. Experimental data regarding mitotic recombination rates or the variations of dCTPs and dGTPs during S phase are required to validate definitively one of the two models, but in any case, the fit of the models to the data suggests that C. albicans and C. dubliniensis constitute so far unique examples of GC content evolution driven either by mitotic recombination or replicative errors.
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Glémin S, Clément Y, David J, Ressayre A. GC content evolution in coding regions of angiosperm genomes: a unifying hypothesis. Trends Genet 2014; 30:263-70. [PMID: 24916172 DOI: 10.1016/j.tig.2014.05.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/09/2014] [Accepted: 05/13/2014] [Indexed: 01/06/2023]
Abstract
In angiosperms (as in other species), GC content varies along and between genes, within a genome, and between genomes of different species, but the reason for this distribution is still an open question. Grass genomes are particularly intriguing because they exhibit a strong bimodal distribution of genic GC content and a sharp 5'-3' decreasing GC content gradient along most genes. Here, we propose a unifying model to explain the main patterns of GC content variation at the gene and genome scale. We argue that GC content patterns could be mainly determined by the interactions between gene structure, recombination patterns, and GC-biased gene conversion. Recent studies on fine-scale recombination maps in angiosperms support this hypothesis and previous results also fit this model. We propose that our model could be used as a null hypothesis to search for additional forces that affect GC content in angiosperms.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, UMR 5554 CNRS, Université Montpellier 2, F-34095 Montpellier, France.
| | - Yves Clément
- Institut des Sciences de l'Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, UMR 5554 CNRS, Université Montpellier 2, F-34095 Montpellier, France; Montpellier SupAgro, Unité Mixte de Recherche 1334 Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398 Montpellier, France
| | - Jacques David
- Montpellier SupAgro, Unité Mixte de Recherche 1334 Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-34398 Montpellier, France
| | - Adrienne Ressayre
- INRA, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParistech, Ferme du Moulon, F-91190 Gif sur Yvette, France
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Giraut L, Falque M, Drouaud J, Pereira L, Martin OC, Mézard C. Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS Genet 2011; 7:e1002354. [PMID: 22072983 PMCID: PMC3207851 DOI: 10.1371/journal.pgen.1002354] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 09/08/2011] [Indexed: 11/19/2022] Open
Abstract
In most species, crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in Arabidopsis thaliana, in male and female meiosis. We observed dramatic differences between male and female meiosis which included: (i) genetic map length; 575 cM versus 332 cM respectively; (ii) CO distribution patterns: male CO rates were very high at both ends of each chromosome, whereas female CO rates were very low; (iii) correlations between CO rates and various chromosome features: female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements (TEs) density, whereas male CO rates correlated positively with the CpG ratio. However, except for CpG, the correlations could be explained by the unequal repartition of these sequences along the Arabidopsis chromosome. For both male and female meiosis, the number of COs per chromosome correlates with chromosome size expressed either in base pairs or as synaptonemal complex length. Finally, we show that interference modulates the CO distribution both in male and female meiosis.
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Affiliation(s)
- Laurène Giraut
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Matthieu Falque
- UMR de Génétique Végétale du Moulon, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Gif sur Yvette, France
| | - Jan Drouaud
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Lucie Pereira
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Olivier C. Martin
- UMR de Génétique Végétale du Moulon, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Gif sur Yvette, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- * E-mail:
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