Where to Cross Over? Defining Crossover Sites in Plants

Dluzewska, Julia; Szymańska, M; Ziolkowski, Piotr A

doi:10.3389/fgene.2018.00609

Cited by 28 publications

(23 citation statements)

References 230 publications

(381 reference statements)

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“…DNA methylation is known to be important in modulating recombination rates in the model plant A. thaliana , which is realized in a strong anticorrelation between recombination rates and DNA methylation (Yelina et al , ; Zhao et al , ; Choi et al , ; Dluzewska et al , ; Tock and Henderson, ; Underwood et al , ). In line with that, we found that recombination rate and the level of DNA methylation were significantly anticorrelated, both in M. polymorpha and P. patens .…”

Section: Discussionmentioning

confidence: 99%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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Summary Marchantia polymorpha has recently become a prime model for cellular, evo‐devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule‐scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high‐density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map‐based cloning, feasible.

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Section: Discussionmentioning

confidence: 99%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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“…The distribution of gametic COs is also known to be affected by variation in heterozygosity, with localised recombination frequency being dependent on factors including chromatin structure and repair mechanisms 54 . Recombination suppression may also be observed as a result of a heterozygous state in cis, with varying homolog polymorphism shaping meiotic recombination [67][68][69] . Heterozygosity is reportedly high in macadamia cultivars and wild accessions 22,[70][71][72][73][74] .…”

Section: Crossover Frequency and Recombination Varied Between Maps Dmentioning

confidence: 99%

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Langdon

King

Baten

et al. 2020

Sci Rep

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the proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.

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“…Consequently, at any given location in the genome, there is general correspondence between the frequency of DSBs and the frequency of recombinants. In many, diverse taxa (e.g., fungi, plants, vertebrates), the DSBs and recombination events cluster at "hotspots" that regulate the frequency and distribution of recombination across the genome (4)(5)(6)(7) .…”

Section: Introductionmentioning

confidence: 99%

Molecular mechanisms for environmentally induced plasticity in the positioning of meiotic recombination at hotspots

Mukiza

Protacio

Davidson

et al. 2020

Preprint

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In meiosis, Spo11/Rec12-initiated homologous recombination is clustered at hotspots that regulate its frequency and distribution across the genome. Intriguingly, the intensities and positions of recombination hotspots can change dramatically in response to intracellular and extracellular conditions, and can display epigenetic memory. Here, using the fission yeast Schizosaccharomyces pombe, we reveal mechanisms for hotspot plasticity. We show that each of six hotspot-activating proteins (transcription factors Atf1, Pcr1, Php2, Php3, Php5, Rst2) is rate-limiting for promoting recombination at its own DNA binding site, allowing each class of hotspot to be regulated independently by agonistic and antagonistic signals. We also discovered that the regulatory protein-DNA complexes can establish a recombinationally poised epigenetic state before meiosis. Notably, Atf1 and Pcr1 controlled the activation of DNA sequence-dependent hotspots to which they do not bind; and they do so by regulating the expression of other hotspot-activating proteins. Thus, while each transcription factor activates its own class of DNA sequence-dependent hotspots directly in cis, cross-talk between regulatory networks modulates in trans the frequency and positioning of recombination at other classes of DNA sequence-dependent hotspots. We posit that such mechanisms allow cells to alter the frequency distribution of meiotic recombination in response to metabolic states and environmental cues.

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Where to Cross Over? Defining Crossover Sites in Plants

Cited by 28 publications

References 230 publications

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Molecular mechanisms for environmentally induced plasticity in the positioning of meiotic recombination at hotspots

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