An Ultra High-Density Arabidopsis thaliana Crossover Map That Refines the Influences of Structural Variation and Epigenetic Features
Beth A. Rowan,Darren Heavens,Tatiana R. Feuerborn,Andrew J. Tock,Ian R. Henderson,Detlef Weigel +5 more
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It is concluded that suppression of COs occurs over a narrow region spanning large- and small-scale SVs, representing an influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.Abstract:
Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of >17,000 COs between the Col-0 and Ler-0 accessions of Arabidopsis thaliana COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large- and small-scale SVs, representing an influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.read more
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A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation
Claire Mérot,Rebekah A. Oomen,Rebekah A. Oomen,Anna Tigano,Maren Wellenreuther,Maren Wellenreuther +5 more
TL;DR: How different types of SVs affect ecological and evolutionary processes are reviewed; unifying definitions and recommendations for future studies are suggested; and a roadmap for the integration of SV's in ecoevolutionary studies is provided.
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Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics
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CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.
Dave Baker,Alp Aydin,Thanh Le-Viet,Gemma L. Kay,Steven Rudder,Leonardo de Oliveira Martins,Ana P. Tedim,Anastasia Kolyva,Anastasia Kolyva,Maria Diaz,Nabil-Fareed Alikhan,Lizzie Meadows,Andrew Bell,Ana Victoria Gutierrez,Alexander J. Trotter,Alexander J. Trotter,Nicholas M. Thomson,Rachel Gilroy,Luke Griffith,Evelien M. Adriaenssens,Rachael Stanley,Ian G. Charles,Ian G. Charles,Ngozi Elumogo,Ngozi Elumogo,John Wain,John Wain,Reenesh Prakash,Emma Meader,Alison E. Mather,Alison E. Mather,Mark A. Webber,Mark A. Webber,Samir Dervisevic,Andrew J. Page,Justin O'Grady,Justin O'Grady +36 more
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Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering
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