Evolutionary mysteries in meiosis

Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often ‘weird’ features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.</p

Energy supply of countryside based on geothermal deposit

Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including epigenetic organization, for example methylation of the DNA and histones. Here we investigate the role of DNA methylation in determining patterns of CO frequency along Arabidopsis thaliana chromosomes. In A. thaliana the pericentromeric regions are repetitive, densely DNA methylated, and suppressed for both RNA polymerase-II transcription and CO frequency. DNA hypomethylated methyltransferase1 (met1) mutants show transcriptional reactivation of repetitive sequences in the pericentromeres, which we demonstrate is coupled to extensive remodeling of CO frequency. We observe elevated centromere-proximal COs in met1, coincident with pericentromeric decreases and distal increases. Importantly, total numbers of CO events are similar between wild type and met1, suggesting a role for interference and homeostasis in CO remodeling. To understand recombination distributions at a finer scale we generated CO frequency maps close to the telomere of chromosome 3 in wild type and demonstrate an elevated recombination topology in met1. Using a pollen-typing strategy we have identified an intergenic nucleosome-free CO hotspot 3a, and we demonstrate that it undergoes increased recombination activity in met1. We hypothesize that modulation of 3a activity is caused by CO remodeling driven by elevated centromeric COs. These data demonstrate how regional epigenetic organization can pattern recombination frequency along eukaryotic chromosomes

Epigenetic Remodeling of Meiotic Crossover Frequency in Arabidopsis thaliana DNA Methyltransferase Mutants

Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction. During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover (CO). Meiotic CO frequency varies along the physical length of chromosomes and is determined by hierarchical mechanisms, including epigenetic organization, for example methylation of the DNA and histones. Here we investigate the role of DNA methylation in determining patterns of CO frequency along Arabidopsis thaliana chromosomes. In A. thaliana the pericentromeric regions are repetitive, densely DNA methylated, and suppressed for both RNA polymerase-II transcription and CO frequency. DNA hypomethylated methyltransferase1 (met1) mutants show transcriptional reactivation of repetitive sequences in the pericentromeres, which we demonstrate is coupled to extensive remodeling of CO frequency. We observe elevated centromere-proximal COs in met1, coincident with pericentromeric decreases and distal increases. Importantly, total numbers of CO events are similar between wild type and met1, suggesting a role for interference and homeostasis in CO remodeling. To understand recombination distributions at a finer scale we generated CO frequency maps close to the telomere of chromosome 3 in wild type and demonstrate an elevated recombination topology in met1. Using a pollen-typing strategy we have identified an intergenic nucleosome-free CO hotspot 3a, and we demonstrate that it undergoes increased recombination activity in met1. We hypothesize that modulation of 3a activity is caused by CO remodeling driven by elevated centromeric COs. These data demonstrate how regional epigenetic organization can pattern recombination frequency along eukaryotic chromosomes

Genotyping Data Hyperrecombinant offspring VIGS

Offspring generated from the crosses of F1 lerxcol plants in which RECQ4 and/or FIGL1 were pressumably knocked-down. Expected lines were expected to be hyperrecombinant but they display the same recombination events as compared to a wild-type population. The genoyping markers used can be seen in the first two rows while the first two columns display the total number of lines used. The markers in blue (B) corresopnd to homozygous Ler alleles while the green ones (H) correspond to the presence of a Col-Ler alleles

Genotyping data MiMe offspring VIGS

Genotyping data regarding the offpsring generated from crosses of F1LerxCol hybrids to the transgenic line male sterile Ler. The genotyping markers used for genotyping are listed in the first rows. The first two columns contain the different lines genotyped. The blue color (B) identify a marker corresponding to a homozygous Ler allele while the green marker (H) corresponds to heterozygous Col-Ler

Reciprocal cybrids reveal how organellar genomes affect plant phenotypes

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Total crossover numbers are similar between wild type and <i>met1–3.</i>

<p>(A) Physical maps of chromosomes (vertical black lines) with KASPar marker (horizontal black lines) and centromere (horizontal red lines) positions indicated. Histograms showing the frequency of total CO numbers identified in male backcross individuals from either Col/Ler F₁ (wild type) or <i>met1–3^−/−</i> Col/Ler F₁ (<i>met1–3</i>) parents. (B) Micrographs of DAPI-stained anther meiocytes showing the labeled stage of meiosis in Col and <i>met1–3^−/−</i>. (C) Micrographs of diplotene and diakineses stage male meiocytes stained with DAPI (white) and immunostained for MLH1 (green). (D) Micrographs showing co-localisation of dense-DAPI staining and <i>in situ</i> hybridization with the <i>CEN180</i> satellite repeat (red). (E) Micrographs of male meiocytes stained with DAPI (white) and immunostained with MLH1 (green) and the axis component ASY1 (red). (F) The upper table lists mean MLH1 foci numbers in wild type and <i>met1–3^−/−</i> at diplotene or diakinesis with standard deviation (+/−). The lower table lists the relative proportions (%) of MLH1 foci localizing to chromosome arm regions (arms) vs densely-DAPI staining regions (DAPI-dense). All scale bars represent 10 µM. See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002844#pgen.1002844.s006" target="_blank">Table S4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002844#pgen.1002844.s007" target="_blank">S5</a>.</p

Decreased pericentromeric crossovers in <i>met1–3</i>.

<p>(A) Physical map of chromosome 3 with overlaid genes/Mb (green), cM/Mb (red) and DNA methylation (blue) plots. The dotted, horizontal red line indicates the cM/Mb weighted mean. Outer vertical black lines indicate the position of FTL transgene insertions that define <i>CEN3</i>. Inner vertical black lines indicate the position of centromeric markers analyzed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002844#pgen-1002844-g002" target="_blank">Figure 2</a>. The vertical magenta line indicates the centromere. (B) Chromosomes heterozygous for <i>trans-</i>linked <i>FTL332</i> (eYFP) and <i>FTL2536</i> (DsRed) transgenes, which flank the centromere (black circle) segregating through meiosis-I and –II in the absence (left) or presence (right) of a CO within <i>CEN3</i>. (C) Fluorescence micrographs of <i>qrt1–2</i> pollen showing patterns of inheritance associated with (tetratype) or without (parental ditype) a CO within <i>CEN3</i>. BF shows bight field illumination and R and G indicate red and green UV fluorescence. (D) <i>CEN3</i> genetic map lengths for naïve wild type (Col), <i>MET1</i>, <i>met1–3^+/−</i>, <i>met1–3^−/−</i> segregants and self-fertilized <i>met1–3^−/−</i> measured by <i>qrt1–2^−/−</i> tetrad counting. (E) Southern blotting and hybridization analysis of <i>CEN180</i> following digestion of genomic DNA using DNA methylation sensitive <i>HpaII</i>. DNA was prepared from <i>CEN3 qrt1–2^−/−</i> individuals whose measured genetic distance in cM is indicated above the blot in blue in addition to their <i>met1–3</i> genotype. See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002844#pgen.1002844.s005" target="_blank">Table S3</a>.</p

Elevated centromeric crossovers in <i>met1–3.</i>

<p>(A) Schematic diagram illustrating generation of wild type and <i>met1–3^−/−</i> recombinant male backcross populations from Col and Ler homozygous parents. (B) Chromosome physical maps with overlaid cM/Mb (red) and DNA methylation (blue) plots; black vertical lines indicate the position of polymorphic Col/Ler markers tested for segregation frequency. Vertical magenta lines indicate centromeres. (C) Segregation data and centromeric CO measurements in wild type and <i>met1–3^−/−</i> male backcross populations.</p

Elevated crossover hotspot <i>3a1</i> activity in <i>met1–3</i>.

<p>(A) CO frequency distributions (cM/Mb, blue) within <i>420</i> map interval 8 measured by dCAPs PCR marker segregation (white bars represent genes, with triangles indicating strand). (B) Plots of cM/Mb for the <i>3a</i> CO hotspot shown for wild type and <i>met1–3^−/−.</i> Vertical black lines indicate the position of the inner PCR primers used to amplify <i>3a</i>. Epigenomic annotation of the <i>3a</i> region with plots displaying low nucleosome density, histone H3K4m (black), H3K4m2 (red) H3K4m3 (green) and DNA methylation densities. (C) Table summarizing quantification of <i>3a</i> parental and CO molecule amplifications from pollen genomic DNA and calculation of cM, cM/Mb and associated standard deviations (S.D.). (D) RNA-seq RPKM (total counts mapping to gene/length of gene×total mapped reads, multiplied by 10⁶) for <i>3a</i> associated genes in wild type (Col) and <i>met1–3</i>. See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002844#pgen.1002844.s012" target="_blank">Table S10</a>.</p