Gregory P. Copenhaver

Venus flytrap ( Dionaea muscipula ) is an insectivorous plant in the monotypic genus Dionaea , endemic to the Southeastern United States, and found in a small geographic range in North and South Carolina. Its unique morphology and natural history have intrigued biologists for centuries, yet the evolution of populations has not been adequately characterized. Population decline, driven primarily by disruptive land conversion, fire suppression, and illegal harvesting/poaching underscores the urgency of defining the genetic diversity in the present population to guide species conservation. We applied a genome-wide SNP dataset to analyze admixture and population structure and used coalescent modeling to trace the ancestry and migration of geographically distinct population clusters. Our population dynamics model supports four lineages, with the North Cape Fear Arch lineage as the ancestor of all lineages and two genetically distinct Sandhills lineages derived from the South Cape Fear Arch lineage independently at ∼13 Ma and ∼3 Ma, respectively, during peak climate optima periods and maximal sea level rise. Severe population decline events occurred among all lineages, with two ancient instant bottleneck population decline events in Sandhills lineages and two recent ones in the two Cape Fear Arch lineages, which contributed to the current genetic structure. Shorter peduncle lengths in Sandhills populations correspond with suspected local adaptation to Sandhills habitats.

Most sexually reproducing eukaryotes use a specialized cell division called meiosis to halve the complement of chromosomes in their gametes. During meiotic prophase I, homologous chromosomes (homologs) recombine by reciprocally exchanging DNA to form cross-overs (COs) that are required for accurate chromosome segregation. COs also reshuffle parental genomes to create genetic diversity among progeny. Molecular genetic studies have identified hundreds of genes involved in meiotic recombination, which have been well summarized in several reviews. Here, we highlight recent advances in understanding endogenous mechanisms that regulate the frequency and distribution of meiotic COs, also called CO patterning. Specifically, we focus on genome-wide regulation, epigenetic control, transcription regulation, and post-transcription processes. Additionally, we highlight open questions that still need further investigation in this field.

Faithful chromosome segregation is essential for both mitotic and meiotic cell division. The anaphase-promoting complex/cyclosome (APC/C) and its coactivators are required for meiotic chromosome segregation, but their potential targets and regulatory mechanisms remain unclear in plants. Here, we performed a ubiquitinome analysis and show that Arabidopsis thaliana Aurora 1 (AUR1) is over-ubiquitinated at lysine 102 in the coactivator Cell Division Cycle 20.1 (cdc20.1) mutants and that AUR1 overexpression can partially rescue the cdc20.1 meiotic defect. We also demonstrate that APC/C ubiquitinates AUR1, leading to its degradation through the 26S proteasome pathway. Moreover, the APC/C subunit and coactivators Cell Cycle Switch 52 A2/B (CCS52A2/B) and CDC20.1 interact with AUR1 both in vitro and in vivo. Intriguingly, CCS52A2/B promotes AUR1 ubiquitination and degradation, while CDC20.1 prevents AUR1 degradation. Consistent with this finding, AUR1 levels are lower in cdc20.1 and higher in ccs52 mutants relative to Col-0, and mutation of CCS52A2/B causes defects in meiotic spindle assembly and homologous chromosome segregation. Genetic analyses demonstrate that Arabidopsis anaphase-promoting complex/cyclosome subunit 8 (APC8), CDC20.1, CCS52 and AUR1 act in the same pathway to control meiotic spindle assembly and homologous chromosome segregation. Thus, this work provides mechanistic insight into the role of APC/C coactivators in regulating AUR1 homeostasis during meiosis in plants.

Meiotic recombination requires the specific RecA homolog DMC1 recombinase to stabilize strand exchange intermediates in most eukaryotes. Normal DMC1 levels are crucial for its function, yet the regulatory mechanisms of DMC1 stability are unknown in any organism. Here, we show that the degradation of Arabidopsis DMC1 by the 26S proteasome depends on F-box proteins RMF1/2-mediated ubiquitination. Furthermore, RMF1/2 interact with the Skp1 ortholog ASK1 to form the ubiquitin ligase complex SCF^RMF1/2. Genetic analyses demonstrate that RMF1/2, ASK1 and DMC1 act in the same pathway downstream of SPO11-1 dependent meiotic DNA double strand break formation and that the proper removal of DMC1 is crucial for meiotic crossover formation. Moreover, six DMC1 lysine residues were identified as important for its ubiquitination but not its interaction with RMF1/2. Our results reveal mechanistic insights into how the stability of a key meiotic recombinase that is broadly conserved in eukaryotes is regulated.

Since Antonie van Leeuwenhoek first observed microbes, we have come to learn that life on our planet includes not only the macroscopic lifeforms visible to the unaided eye that Charles Darwin studied but also an immense diversity of microbes (Fig 1). We have learned that microorganisms influence nearly every aspect of human existence with beneficial or detrimental effects. With their pivotal roles in biomass conversion, biogeochemical cycles, photosynthesis, and in promoting plant growth, life on this planet ultimately depends on the activities of microorganisms. On the other hand, microorganisms are the etiological agents of many diseases in humans, animals, and plants, causing massive economic losses yearly. Microorganisms also contribute significantly to the production of greenhouse gases such as CO 2 and CH 4 and, thus, contribute to global warming. In the past decade, we have also learned that microorganisms inhabiting the human body, i.e., the human microbiome, have profound effects on human physiology. Not to forget, some of our most delicious food products and beverages get their distinct qualities from microorganisms, and the pharmaceutical and biotechnological industry relies heavily on microbes. In terms of research, many technological breakthroughs in molecular biology, such as DNA cloning, PCR, and CRISPR-Cas technologies have their origin in microbes. Therefore, research in microbiology is as important now as it ever was. Research on microbes has developed at a breathtaking pace. Genetic systems have been established in many microbes, and the advent of omics technologies allows studying microbes without established genetic systems. To reflect the importance of microbes and to create a home for microbiology research using genetics, PLOS Genetics will be launching a new section on Microbial Genetics. This section will replace the former Prokaryotic Genetics section to emphasize research on microbes more broadly. The new section on Microbial Genetics will cover research on bacteria as well as archaea and their phages/viruses, fungi (including yeasts and filamentous fungi), and protists. We aim to publish studies that use genetic approaches to provide insights of broad significance into how microbes function and interact with the biotic and abiotic world. Manuscripts on genome evolution, comparative genomics, metagenomics, and microbiomes that increase our understanding of microbial diversity will also be included in this new section. Such manuscripts are generally expected to either include functional validation or report a clear genotype-phenotype relationship.

Heterochromatin is essential for genomic integrity and stability in eukaryotes. The mechanisms that regulate meiotic heterochromatin formation remain largely undefined. Here, we show that the catalytic subunit (POL2A) ofArabidopsisDNA polymerase epsilon (POL ε) is required for proper formation of meiotic heterochromatin. The POL2A N terminus interacts with the GHKL adenosine triphosphatase (ATPase) MORC1 (Microrchidia 1), and POL2A is required for MORC1’s localization on meiotic heterochromatin. Mutations affecting the POL2A N terminus cause aberrant morphology of meiotic heterochromatin, which is also observed inmorc1. Moreover, the POL2A C-terminal zinc finger domain (ZF1) specifically binds to histone H3.1-H4 dimer or tetramer and is important for meiotic heterochromatin condensation. Interestingly, we also found similar H3.1-binding specificity for the mouse counterpart. Together, our results show that two distinct domains of POL2A, ZF1 and N terminus bind H3.1-H4 and recruit MORC1, respectively, to induce a continuous process of meiotic heterochromatin organization. These activities expand the functional repertoire of POL ε beyond its classic role in DNA replication and appear to be conserved in animals and plants.

Meiotic recombination is initiated by the SPORULATION 11 (SPO11)–triggered formation of double-strand breaks (DSBs) that usually occur in open chromatin with active transcriptional features in many eukaryotes. However, gene transcription at DSB sites appears to be detrimental for repair, but the regulatory mechanisms governing transcription at meiotic DSB sites are largely undefined in plants. Here, we demonstrate that the largest DNA polymerase epsilon subunit POL2A interacts with SU(VAR)3 to 9 homologs SUVH2 and SUVH9. N-SIM (structured illumination microscopy) observation shows that the colocalization of SUVH2 with the meiotic DSB marker γ-H2AX is dependent on POL2A. RNA-seq of male meiocytes demonstrates that POL2A and SUVH2 jointly repress the expression of 865 genes, which have several known characteristics associated with meiotic DSB sites. Bisulfite-seq and small RNA-seq of male meiocytes support the idea that the silencing of these genes by POL2A and SUVH2/9 is likely independent of CHH methylation or 24-nt siRNA accumulation. Moreover, pol2a suvh2 suvh9 triple mutants have more severe defects in meiotic recombination and fertility compared with either pol2a or suvh2 suvh9 . Our results not only identify a epigenetic regulatory mechanism for gene silencing in male meiocytes but also reveal roles for DNA polymerase and SUVH2/9 beyond their classic functions in mitosis.

Meiosis is a specialized cell division that generates gametes and is essential for sexual reproduction. Studying meiosis in plants, like the model flowering plant Arabidopsis thaliana, contributes to our understanding of the fundamental biology of reproductive biology and has practical implications for improving economically important crop species. In this chapter, we provide a detailed protocol for capillary collection of Arabidopsis male meiocytes followed by total RNA extraction, RNA-Seq, and bioinformatics analysis of small-RNAs (sRNAs) including analysis of sRNA cluster that correlate with genomic features.

Histone methylation and demethylation play important roles in plant growth and development, but the involvement of histone demethylation during meiosis is poorly understood. Here we show that disruption ofArabidopsis thaliana INCREASE IN BONSAI METHYLATION 1(IBM1) causes incomplete synapsis, chromosome entanglement and reduction of recombination during meiosis, leading to sterility. Interestingly, theseibm1meiotic defects are rescued by mutations in eitherSUVH4/KYPorCMT3. Using transcriptomic analyses we show that mutation of IBM1 down-regulates thousands of genes expressed in meiocytes, and that expression of about 38% of these genes are restored to wild type levels inibm1 cmt3double mutants. Changes in the expression of 437 of these, including theARABIDOPSIS MEI2-LIKE AML3-5genes, are correlated with a significant reduction of gene body CHG methylation. Consistently, theaml3 aml4 aml5triple have defects in synapsis and chromosome entanglement similar toibm1. Genetic analysis shows thataml3 aml4 aml5 ibm1quadruple mutants resembles theibm1single mutant. Strikingly, over expression ofAML5inibm1can partially rescue theibm1meiotic defects. Taken together, our results demonstrate that histone demethylase IBM1 is required for meiosis likely via coordinated regulation of meiocyte gene expression during meiosis.