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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...frequency (Westphal and Reuter 2002). Interestingly, the A. thaliana met1 and ddm1 CG methylation mutants associate with remodeling of meiotic recombination along chromosomes, with crossover increases in the chromosome arms and decreases across the pericentromeres (Colomé-Tatché et al. 2012; Melamed...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core . We use the high density of SNP and indel markers to analyze patterns of meiotic recombination...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
...chromatin state and genetic variation across crossover-rate gradients.ResultsDMC1 recombinase colocalizes with the meiotic axis protein ASY1We used polyclonal antibodies raised against Arabidopsis DMC1 in rabbit (Sanchez-Moran et al. 2007) and the recombinant wheat ASY1 HORMA domain in guinea pig...
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Research: Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
- Pingli Lu,
- Xinwei Han,
- Ji Qi,
- Jiange Yang,
- Asela J. Wijeratne,
- Tao Li,
- and Hong Ma
Genome Res. March 2012 22: 508-518; Published in Advance November 21, 2011, doi:10.1101/gr.127522.111
...detected 18 COs, six of which had an associated GC event, and four GCs without COs (NCOs), and revealed that Arabidopsis GCs are likely fewer and with shorter tracts than those in yeast. Meiotic recombination and chromosome assortment events dramatically redistributed variation in meiotic products...
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Research: The recombination landscape of the zebra finch Taeniopygia guttata genome
- Niclas Backström,
- Wolfgang Forstmeier,
- Holger Schielzeth,
- Harriet Mellenius,
- Kiwoong Nam,
- Elisabeth Bolund,
- Matthew T. Webster,
- Torbjörn Öst,
- Melanie Schneider,
- Bart Kempenaers,
- and Hans Ellegren
Genome Res. April 2010 20: 485-495; Published in Advance March 31, 2010, doi:10.1101/gr.101410.109
.... The distribution of recombination rates was heavily skewed with a large proportion of windows showing no recombination (Fig. 1). A closer inspection of the variation in recombination rate along chromosomes revealed a sharp increase toward telomeric regions. Moreover, there were extremely low rates of recombination...
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LETTER: The 1.4-Mb CMT1A Duplication/HNPP Deletion Genomic Region Reveals Unique Genome Architectural Features and Provides Insights into the Recent Evolution of New Genes
- Ken Inoue,
- Ken Dewar,
- Nicholas Katsanis,
- Lawrence T. Reiter,
- Eric S. Lander,
- Keri L. Devon,
- Dudley W. Wyman,
- James R. Lupski,
- and Bruce Birren
Genome Res. June 1, 2001 11: 1018-1033; doi:10.1101/gr.180401
...(5.5 cM/Mb). Hypothetically, this low recombination frequency in males may enable a chromosomal misalignment at proximal and distal CMT1A–REPs and promote unequal crossing over, which occurs 10 times more frequently in male meiosis. In addition to three previously described genes, five new genes...
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Resource: A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci
- Kaitlin U. Laverty,
- Jake M. Stout,
- Mitchell J. Sullivan,
- Hardik Shah,
- Navdeep Gill,
- Larry Holbrook,
- Gintaras Deikus,
- Robert Sebra,
- Timothy R. Hughes,
- Jonathan E. Page,
- and Harm van Bakel
Genome Res. January 2019 29: 146-156; Published in Advance November 8, 2018, doi:10.1101/gr.242594.118
...species, including maize (Liu et al. 2009) and Arabidopsis thaliana (Choi et al. 2013), this arrangement may underlie the observed recombination frequencies. Third, the poorly recombining central parts of chromosomes not only are gene-poor but also have a higher repeat content, which may be methylated...
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Research: Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
- Florent Murat,
- Jian-Hong Xu,
- Eric Tannier,
- Michael Abrouk,
- Nicolas Guilhot,
- Caroline Pont,
- Joachim Messing,
- and Jérôme Salse
Genome Res. November 2010 20: 1545-1557; Published in Advance September 28, 2010, doi:10.1101/gr.109744.110
..., and number of orthologous genes. These data clearly confirmed that the recombination pattern (i.e., CO for crossing-over) of the chromosome was directly linked to gene density, gene conservation, and SBPs. It became clear that gene shuffling (duplication or loss resulting in lower syntenic content) took...
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Research: High mutational rates of large-scale duplication and deletion in Daphnia pulex
- Nathan Keith,
- Abraham E. Tucker,
- Craig E. Jackson,
- Way Sung,
- José Ignacio Lucas Lledó,
- Daniel R. Schrider,
- Sarah Schaack,
- Jeffry L. Dudycha,
- Matthew Ackerman,
- Andrew J. Younge,
- Joseph R. Shaw,
- and Michael Lynch
Genome Res. January 2016 26: 60-69; Published in Advance October 30, 2015, doi:10.1101/gr.191338.115
...crossing over during recombination (Read et al. 2004). Thus, the total rate of gene duplication and deletion in D. pulex may be higher than the estimates we provide. The difference in mutation rates between ASEX and CYC is also of interest. Relative to the CYC lines, in the ASEX experiment, the base...
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Research: Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
- Konstantinos Kritsas,
- Samuel E. Wuest,
- Daniel Hupalo,
- Andrew D. Kern,
- Thomas Wicker,
- and Ueli Grossniklaus
Genome Res. December 2012 22: 2455-2466; Published in Advance September 17, 2012, doi:10.1101/gr.129346.111
...and replication. Indeed, it was shown that sequences with many ATs and TAs have lower recombination rates than those containing AGs, TCs, CAs, and TGs (Guo et al. 2009). Thus, we explored the possibility that ULEs are enriched at recombination hot spots (RHSs). RHSs are DNA regions with a higher rate of meiotic...
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