The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana
- Wageningen University, Netherlands
- IBMP–CNRS, Université de Strasbourg, France
- Max Planck Institute for Plant Breeding Research, Germany
- Max Planck Institute for Developmental Biology, Germany
- Rijk Zwaan, Netherlands
- Center for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Spain
Figures
Figure 1 with 2 supplements
Experimental design and summary of recombination events within 62 recombinants.
(A) 13 complete tetrads were generated by crossing qrt1 in a Col background to qrt1 in a Ler background, and then using single pollen tetrads from the F1 hybrids to fertilize a Cvi male sterile …
Figure 1—figure supplement 1
Graphical genotypes of all 13 complete tetrads.
For each tetrad, all five chromosomes of all four offspring are shown (chromosome one to five, top to bottom). The four offspring genomes of one tetrad are plotted one above the other. Black lines …
Figure 1—figure supplement 2
Graphical genotypes of 10 DH lines.
For each DH line, all five chromosomes are shown, chromosome one to five (top to bottom). Black lines depict peri-centromeric regions.
Figure 2 with 6 supplements
Identification of gene conversions is complex because of unknown duplications and transpositions in the A. thaliana genome.
(A) Short read alignments of Ler against the reference sequence at position 13,957,178 on chromosome 1. Individual reads are shown as blue lines, while mismatches between reference sequence and …
Figure 2—figure supplement 1
Graphical illustration of short read alignments at type-1 and type-2 markers revealing no NCO–GCs (two loci at the left) and the same loci revealing type-1 and type-2 NCO-GCs (right).
Short read alignments are shown in colors according to the respective genome, if they cannot be uniquely assigned to one unique parent they are shown in grey. At type-1 markers, the expected allele …
Figure 2—figure supplement 2
Observed allele distribution throughout all deeply sequenced tetrad genomes.
Observed allele frequencies (AFs) were derived from allele counts (based on short read alignments) at the respective marker loci. AFs at type-1 markers (homozygous alleles) are shown in red, AFs at …
Figure 2—figure supplement 3
NCO–GC frequency per marker per meiosis measured in the five deeply sequenced tetrads, using a range of minimal coverage thresholds and three different marker sets.
NCO–GC frequency was assessed using different marker sets. Marker sets with more stringent filtering showed a lower frequency of putative NCO–GCs, which indicates that filtering reduces the …
Figure 2—figure supplement 4
The number of putative type-1 and type-2 NCO–GCs in all 20 deeply sequenced tetrad offspring using different marker sets.
Bar charts show the number of NCO–GC detected per offspring plant using different marker set generated with different filter stringencies in each subsequent step (top to bottom). Quality score …
Figure 2—figure supplement 5
Transposed sequences on A. thaliana chromosome 3.
(A) Upper panel shows, analogous to Figure 2B, the location of transposed DNA between the two parental lines Ler and Col. Thin blue and red lines indicate co-linear sequences. Green thick lines show …
Figure 2—figure supplement 6
NCO–GC frequency per marker per meiosis measured in 10 recombinant DH lines at increasing minimal coverage thresholds.
From a minimal coverage threshold of 10 onwards, the observed frequency of putative NCO–GC does not majorly change. This is in contrast to the minimal coverage requirement for the tetrad sample …
Figure 3
Sequence similarity at recombination sites, length differences between COCTs and NCOCTs and crossover interference.
(A) The percentage of confidently aligned positions within the resequencing of Ler was used as proxy for local sequence similarity. The percentages at COs were compared to a background distribution …
Figure 4
Recombination sites are enriched for un-methylated, AT rich promoter regions.
(A) The GC content was calculated for 67 conversion tracts (including 500 bp of flanking sequence, top) and compared to a background distribution of 5,000 equally sized random locations sampled from …
Figure 5
Recombination sites are significantly associated with two sequence motifs and nucleosome-free regions.
(A) Two sequence motifs (poly-A and CTT/GAA) were found significantly enriched at recombination sites after searching for over-enriched motifs using MEME. We established background frequency …
Additional files
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Supplementary file 1
(A) Read number. (B) Number of crossovers per tetrad and DH line and chromosome. (C) CO location. (D) NCO location and extent within the tetrad samples. (E) CO location in DH lines. (F) Exact loci of CO and extent of associated GC in tetrad samples. (G) Converted markers within COCTs in tetrad samples. (H) Converted markers within NCOCTs in DH lines.
- https://doi.org/10.7554/eLife.01426.016
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Supplementary file 2
(A) Initial marker list used for an initial genotyping of the tetrad samples. (B) Filtered marker list used to genotype tetrad samples. (C) High quality marker list used to genotype DH samples. (D) Primer pairs used for verification of NCOs in tetrad offspring. (E) Primer pairs used for verification of NCOs in DH lines. (F) Primers used for the verification of transposed DNA on chromosome 3.
- https://doi.org/10.7554/eLife.01426.017
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Supplementary file 3
Includes a visualization of the exact makeup of 71 COs identified in the tetrad samples, for which sufficient sequencing information was available. The colored areas indicate the number of short read alignments for each of the positions as indicated on the x-axis. Red and blue areas refer to regions that descended from Col-0 and Ler, respectively. Grey areas cannot be assigned to either of them. Vertical lines indicate sequence differences between the parental genotypes and have the respective genotype indicated next to them. Within the CO sites (between the outer borders of both grey areas) the polymorphism data are based on hand curated short read alignments and local assemblies. Outside the flanking markers the polymorphisms encompass the marker used for reconstructing the recombinant chromosomes only. Note each tetrad sample contains one recombinant chromosome and one that is derived from the Cvi parent. The Cvi alleles are not indicated in these plots.
- https://doi.org/10.7554/eLife.01426.018
