A Decad(e) of Reasons to Contribute to a PLOS Community-Run Journal

Whether it's the number of primate digits, the number of Vishnu avatars, or the number of items on David Letterman's lists for the last 30 years, humans have an almost inordinate fascination with the number ten. That fascination has been especially apparent at PLOS these past few months, as we and two of our sister journals celebrate our tenth anniversary in close succession. Recalling the wonderful "Ten Simple Rules" articles published in PLOS Computational Biology, we at PLOS Genetics are publishing a Tenth Anniversary Collection of our Top Ten Research Articles published over the last ten years

Scientists←editors←scientists: The past, present, and future of PLoS genetics

PLoS Genetics is different: different not only because of the PLoS-wide vision for open access and new ways of communicating science, but also in terms of administration and leadership. We are, first and foremost, a community journal, where editorial decisions and direction are made by consensus. This model, where responsibility is distributed among a team of more than 80 working scientists in a way that promotes and encourages discussion, has been nourished and developed fully by Wayne Frankel, who has been with the journal since its inception, and first introduced us to PLoS Genetics exactly four years ago. As the founding Editor-in-Chief, Wayne brought us to where we are today—with nearly 150 new submissions per month, a scope that covers the entire tree of life (and occasionally synthetic biology), and a focus on scientific substance together with a goal of serving the interests of both readers and authors. In making the transition from scientist to Editor-in-Chief, and again to scientist earlier this year, Wayne’s contributions have shown how one role can strengthen the other. Happily, he remains an active member of the Editorial Board, shepherding and consulting on manuscripts in the areas of mammalian genetics and neurobiology

Consent and internet-enabled human genomics

This month, PLoS Genetics is publishing an article from the company 23andMe reporting the first genome-wide association studies (GWAS) on multiple traits ascertained by self-reported information provided through the Internet from over 10,000 participants who pay the company for providing whole genome genotypes. The paper passed through scientific review by a panel of three experts relatively quickly and is sure to attract the attention of anyone with freckles, curly hair, or an aversion to asparagus. Novel associations are described for four intrinsically interesting traits (out of 22 considered), while known associations with hair and eye color are replicated in a dynamic data-gathering context. Additionally, intriguing observations on the interaction between genetic self-knowledge and self-report of phenotypes are described. The implications of the successful application of this Internet-enabled approach to GWAS research were considered to be more than sufficient to warrant publication in the journal

The Language of Genetics In the Interviews of Jane Gitschier

"Tell me, what is it you plan to do with your one wild and precious life?" The question that concludes Mary Oliver's poem, The Summer Day, reminds us not only of a poet inspired by her observations of the natural world but also of Jane Gitschier, a scientist, author, musician, and mother whose relationship with and observations of those around her have contributed so much to our community. This editorial is intended to commemorate and celebrate Jane's series of more than 40 interviews published by PLOS Genetics, spanning ten years of publishing, about a billion years of evolution—from Archea to Brassica, from prions to mammals—and a set of themes and ideas that make the word "eclectic" seem puny by comparison

Meiotic Recombination: Mixing It Up in Plants

Meiosis halves diploid chromosome numbers to haploid levels that are essential for sexual reproduction in most eukaryotes. Meiotic recombination ensures the formation of bivalents between homologous chromosomes (homologs) and their subsequent proper segregation. It also results in genetic diversity among progeny that influences evolutionary responses to selection. Moreover, crop breeding depends upon the action of meiotic recombination to rearrange elite traits between parental chromosomes. An understanding of the molecular mechanisms that drive meiotic recombination is important for both fundamental research and practical applications. This review emphasizes advances made during the past 5 years, primarily in Arabidopsis and rice, by summarizing newly characterized genes and proteins and examining the regulatory mechanisms that modulate their action

Meiotic DNA repair in the nucleolus employs a nonhomologous end-joining mechanism

Ribosomal RNA genes are arranged in large arrays with hundreds of rDNA units in tandem. These highly repetitive DNA elements pose a risk to genome stability since they can undergo nonallelic exchanges. During meiosis, DNA double-strand breaks (DSBs) are induced as part of the regular program to generate gametes. Meiotic DSBs initiate homologous recombination (HR), which subsequently ensures genetic exchange and chromosome disjunction. In Arabidopsis (Arabidopsis thaliana), we demonstrate that all 45S rDNA arrays become transcriptionally active and are recruited into the nucleolus early in meiosis. This shields the rDNA from acquiring canonical meiotic chromatin modifications and meiotic cohesin and allows only very limited meiosis-specific DSB formation. DNA lesions within the rDNA arrays are repaired in an RAD51-independent but LIG4-dependent manner, establishing that nonhomologous end-joining maintains rDNA integrity during meiosis. Utilizing ectopically integrated rDNA repeats, we validate our findings and demonstrate that the rDNA constitutes an HR-refractory genome environment

The Role of Chromatid Interference in Determining Meiotic Crossover Patterns

Plants, like all sexually reproducing organisms, create genetic variability by reshuffling parental alleles during meiosis. Patterns of genetic variation in the resulting gametes are determined by the independent assortment of chromosomes in meiosis I and by the number and positioning of crossover (CO) events during meiotic recombination. On the chromosome level, spatial distribution of CO events is biased by multiple regulatory mechanisms, such as CO assurance, interference and homeostasis. However, little is known about how multiple COs are distributed among the four chromatids of a bivalent. Chromatid interference (CI) has been proposed as a regulatory mechanism that biases distribution of multiple COs toward specific chromatid partners, however, its existence has not been well-studied and its putative mechanistic basis remains undescribed. Here, we introduce a novel method to quantitatively express CI, and take advantage of available tetrad-based genotyping data from Arabidopsis and maize male meiosis to quantify CI effects on a genome-wide and chromosomal scale. Overall, our analyses reveal random involvement of sister chromatids in double CO events across paired chromosomes, indicating an absence of CI. However, on a genome-wide level, CI was found to vary with physical distance between COs, albeit with different effects in Arabidopsis and maize. While effects of CI are minor in Arabidopsis and maize, the novel methodology introduced here enables quantitative interpretation of CI both on a local and genome-wide scale, and thus provides a key tool to study CI with relevance for both plant genetics and crop breeding

Expanding human variation at PLOS Genetics

The “experiments of nature” that underlie genetics engage all organisms equally: from microbes and slime molds to plants and vertebrates, the inextricable connection between genotype and phenotype lies at the core of our community. That community is remarkably diverse, spanning an array of not only organisms but also approaches and questions; indeed, diversity is one of the main reasons we enjoy contributing to the journal

New insights into the role of DNA synthesis in meiotic recombination

Meiosis comprises two rounds of nuclear division following a single phase of DNA replication, leading to the production of haploid gametes and is essential for sexual reproduction in eukaryotes. Unlike mitosis, meiosis involves homologous chromosome pairing, synapsis, and recombination during prophase I. Meiotic recombination not only ensures the accurate segregation of homologs, but also redistributes alleles among offspring. DNA synthesis is a critical process during meiotic recombination, but our understanding of the proteins that execute and regulate it is limited. This review summarizes the recent advances in defining the role of DNA synthesis in meiotic recombination through analyses of DNA synthesis genes, with specific emphasis on DNA polymerases (e.g., Polε and Polδ), replication processivity factor RFC1 and translesion polymerases (e.g., Polζ). We also present a new double strand break repair model for meiotic recombination, which includes lagging strand DNA synthesis and leading strand elongation. Finally, we propose that DNA synthesis is one of critical factors for discriminating meiotic recombination pathways and that this differentiation may be conserved among eukaryotes

Comparative transcriptomic analysis of thermally stressed Arabidopsis thaliana meiotic recombination mutants

Background: Meiosis is a specialized cell division that underpins sexual reproduction in most eukaryotes. During meiosis, interhomolog meiotic recombination facilitates accurate chromosome segregation and generates genetic diversity by shuffling parental alleles in the gametes. The frequency of meiotic recombination in Arabidopsis has a U-shaped curve in response to environmental temperature, and is dependent on the Type I, crossover (CO) interference-sensitive pathway. The mechanisms that modulate recombination frequency in response to temperature are not yet known. Results: In this study, we compare the transcriptomes of thermally-stressed meiotic-stage anthers from msh4 and mus81 mutants that mediate the Type I and Type II meiotic recombination pathways, respectively. We show that heat stress reduces the number of expressed genes regardless of genotype. In addition, msh4 mutants have a distinct gene expression pattern compared to mus81 and wild type controls. Interestingly, ASY1, which encodes a HORMA domain protein that is a component of meiotic chromosome axes, is up-regulated in wild type and mus81 but not in msh4. In addition, SDS the meiosis-specific cyclin-like gene, DMC1 the meiosis-specific recombinase, SYN1/REC8 the meiosis-specific cohesion complex component, and SWI1 which functions in meiotic sister chromatid cohesion are up-regulated in all three genotypes. We also characterize 51 novel, previously unannotated transcripts, and show that their promoter regions are associated with A-rich meiotic recombination hotspot motifs. Conclusions: Our transcriptomic analysis of msh4 and mus81 mutants enhances our understanding of how the Type I and Type II meiotic CO pathway respond to environmental temperature stress and might provide a strategy to manipulate recombination levels in plants