The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana
Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we...
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| creator | Wijnker, Erik James, Geo Velikkakam Ding, Jia Becker, Frank Klasen, Jonas R Rawat, Vimal Rowan, Beth A de Jong, Daniel F de Snoo, C. Bastiaan Zapata, Luis Huettel, Bruno de Jong, Hans Ossowski, Stephan Weigel, Detlef Koornneef, Maarten Keurentjes, Joost J. B Schneeberger, Korbinian |
| description | Knowledge of the exact distribution of meiotic crossovers (COs) and gene
conversions (GCs) is essential for understanding many aspects of population
genetics and evolution, from haplotype structure and long-distance genetic
linkage to the generation of new allelic variants of genes. To this end, we
resequenced the four products of 13 meiotic tetrads along with 10 doubled
haploids derived from Arabidopsis thaliana hybrids. GC detection through short
reads has previously been confounded by genomic rearrangements. Rigid filtering
for misaligned reads allowed GC identification at high accuracy and revealed an
~80-kb transposition, which undergoes copy-number changes mediated by meiotic
recombination. Non-crossover associated GCs were extremely rare most likely due
to their short average length of ~25-50 bp, which is significantly shorter than
the length of CO associated GCs. Overall, recombination preferentially targeted
non-methylated nucleosome-free regions at gene promoters, which showed
significant enrichment of two sequence motifs. |
| doi_str_mv | 10.48550/arxiv.1311.3236 |
| format | Article |
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conversions (GCs) is essential for understanding many aspects of population
genetics and evolution, from haplotype structure and long-distance genetic
linkage to the generation of new allelic variants of genes. To this end, we
resequenced the four products of 13 meiotic tetrads along with 10 doubled
haploids derived from Arabidopsis thaliana hybrids. GC detection through short
reads has previously been confounded by genomic rearrangements. Rigid filtering
for misaligned reads allowed GC identification at high accuracy and revealed an
~80-kb transposition, which undergoes copy-number changes mediated by meiotic
recombination. Non-crossover associated GCs were extremely rare most likely due
to their short average length of ~25-50 bp, which is significantly shorter than
the length of CO associated GCs. Overall, recombination preferentially targeted
non-methylated nucleosome-free regions at gene promoters, which showed
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conversions (GCs) is essential for understanding many aspects of population
genetics and evolution, from haplotype structure and long-distance genetic
linkage to the generation of new allelic variants of genes. To this end, we
resequenced the four products of 13 meiotic tetrads along with 10 doubled
haploids derived from Arabidopsis thaliana hybrids. GC detection through short
reads has previously been confounded by genomic rearrangements. Rigid filtering
for misaligned reads allowed GC identification at high accuracy and revealed an
~80-kb transposition, which undergoes copy-number changes mediated by meiotic
recombination. Non-crossover associated GCs were extremely rare most likely due
to their short average length of ~25-50 bp, which is significantly shorter than
the length of CO associated GCs. Overall, recombination preferentially targeted
non-methylated nucleosome-free regions at gene promoters, which showed
significant enrichment of two sequence motifs.</description><subject>Quantitative Biology - Genomics</subject><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>GOX</sourceid><recordid>eNotjztrwzAUhbVkKEn3TkV_wK7kK8vyGEJfEOjQDN3MtXzVCGzJSCG0_7522-lwHhz4GLuTolSmrsUDpi9_LSVIWUIF-oZ9nM7EPynEyVs-YhiyxZl4dHwiHy9LaFPMOV4pZb7U65a4jWENfAyZ-8D3CXs_xDn7zC9nHD0G3LGNwzHT7b9u2fvT4-nwUhzfnl8P-2OButaFElpoBFPpxvQSAAYF4LRqakNgXDMI1ZMzsm2pBdtWArXAxtaVcotXsGX3f6-_YN2c_ITpu1sBuxUQfgA3CEsw</recordid><startdate>20131113</startdate><enddate>20131113</enddate><creator>Wijnker, Erik</creator><creator>James, Geo Velikkakam</creator><creator>Ding, Jia</creator><creator>Becker, Frank</creator><creator>Klasen, Jonas R</creator><creator>Rawat, Vimal</creator><creator>Rowan, Beth A</creator><creator>de Jong, Daniel F</creator><creator>de Snoo, C. Bastiaan</creator><creator>Zapata, Luis</creator><creator>Huettel, Bruno</creator><creator>de Jong, Hans</creator><creator>Ossowski, Stephan</creator><creator>Weigel, Detlef</creator><creator>Koornneef, Maarten</creator><creator>Keurentjes, Joost J. B</creator><creator>Schneeberger, Korbinian</creator><scope>ALC</scope><scope>GOX</scope></search><sort><creationdate>20131113</creationdate><title>The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana</title><author>Wijnker, Erik ; James, Geo Velikkakam ; Ding, Jia ; Becker, Frank ; Klasen, Jonas R ; Rawat, Vimal ; Rowan, Beth A ; de Jong, Daniel F ; de Snoo, C. Bastiaan ; Zapata, Luis ; Huettel, Bruno ; de Jong, Hans ; Ossowski, Stephan ; Weigel, Detlef ; Koornneef, Maarten ; Keurentjes, Joost J. B ; Schneeberger, Korbinian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a656-40606a382678b1333d433f64758e38f7d04bef8199e93c920a60a7c524f93c43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Quantitative Biology - Genomics</topic><toplevel>online_resources</toplevel><creatorcontrib>Wijnker, Erik</creatorcontrib><creatorcontrib>James, Geo Velikkakam</creatorcontrib><creatorcontrib>Ding, Jia</creatorcontrib><creatorcontrib>Becker, Frank</creatorcontrib><creatorcontrib>Klasen, Jonas R</creatorcontrib><creatorcontrib>Rawat, Vimal</creatorcontrib><creatorcontrib>Rowan, Beth A</creatorcontrib><creatorcontrib>de Jong, Daniel F</creatorcontrib><creatorcontrib>de Snoo, C. Bastiaan</creatorcontrib><creatorcontrib>Zapata, Luis</creatorcontrib><creatorcontrib>Huettel, Bruno</creatorcontrib><creatorcontrib>de Jong, Hans</creatorcontrib><creatorcontrib>Ossowski, Stephan</creatorcontrib><creatorcontrib>Weigel, Detlef</creatorcontrib><creatorcontrib>Koornneef, Maarten</creatorcontrib><creatorcontrib>Keurentjes, Joost J. B</creatorcontrib><creatorcontrib>Schneeberger, Korbinian</creatorcontrib><collection>arXiv Quantitative Biology</collection><collection>arXiv.org</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Wijnker, Erik</au><au>James, Geo Velikkakam</au><au>Ding, Jia</au><au>Becker, Frank</au><au>Klasen, Jonas R</au><au>Rawat, Vimal</au><au>Rowan, Beth A</au><au>de Jong, Daniel F</au><au>de Snoo, C. Bastiaan</au><au>Zapata, Luis</au><au>Huettel, Bruno</au><au>de Jong, Hans</au><au>Ossowski, Stephan</au><au>Weigel, Detlef</au><au>Koornneef, Maarten</au><au>Keurentjes, Joost J. B</au><au>Schneeberger, Korbinian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana</atitle><date>2013-11-13</date><risdate>2013</risdate><abstract>Knowledge of the exact distribution of meiotic crossovers (COs) and gene
conversions (GCs) is essential for understanding many aspects of population
genetics and evolution, from haplotype structure and long-distance genetic
linkage to the generation of new allelic variants of genes. To this end, we
resequenced the four products of 13 meiotic tetrads along with 10 doubled
haploids derived from Arabidopsis thaliana hybrids. GC detection through short
reads has previously been confounded by genomic rearrangements. Rigid filtering
for misaligned reads allowed GC identification at high accuracy and revealed an
~80-kb transposition, which undergoes copy-number changes mediated by meiotic
recombination. Non-crossover associated GCs were extremely rare most likely due
to their short average length of ~25-50 bp, which is significantly shorter than
the length of CO associated GCs. Overall, recombination preferentially targeted
non-methylated nucleosome-free regions at gene promoters, which showed
significant enrichment of two sequence motifs.</abstract><doi>10.48550/arxiv.1311.3236</doi><oa>free_for_read</oa></addata></record> |
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| title | The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana |
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