G3 (Bethesda, Md.)最新文献

{"title":"Linkage mapping reveals loci that underlie differences in Caenorhabditis elegans growth.","authors":"Joy Nyaanga,&nbsp;Erik C Andersen","doi":"10.1093/g3journal/jkac207","DOIUrl":"https://doi.org/10.1093/g3journal/jkac207","url":null,"abstract":"<p><p>Growth rate and body size are complex traits that contribute to the fitness of organisms. The identification of loci that underlie differences in these traits provides insights into the genetic contributions to development. Leveraging Caenorhabditis elegans as a tractable metazoan model for quantitative genetics, we can identify genomic regions that underlie differences in growth. We measured postembryonic growth of the laboratory-adapted wild-type strain (N2) and a wild strain from Hawaii (CB4856) and found differences in body size. Using linkage mapping, we identified three distinct quantitative trait loci (QTL) on chromosomes IV, V, and X that are associated with variation in body growth. We further examined these growth-associated quantitative trait loci using chromosome substitution strains and near-isogenic lines and validated the chromosome X quantitative trait loci. In addition, we generated a list of candidate genes for the chromosome X quantitative trait loci. These genes could potentially contribute to differences in animal growth and should be evaluated in subsequent studies. Our work reveals the genetic architecture underlying animal growth variation and highlights the genetic complexity of growth in Caenorhabditis elegans natural populations.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40609723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of nonautonomous modulators of activated Ras.","authors":"Marcos Corchado-Sonera,&nbsp;Komal Rambani,&nbsp;Kristen Navarro,&nbsp;Raleigh Kladney,&nbsp;James Dowdle,&nbsp;Gustavo Leone,&nbsp;Helen M Chamberlin","doi":"10.1093/g3journal/jkac200","DOIUrl":"https://doi.org/10.1093/g3journal/jkac200","url":null,"abstract":"<p><p>Communication between mesodermal cells and epithelial cells is fundamental to normal animal development and is frequently disrupted in cancer. However, the genes and processes that mediate this communication are incompletely understood. To identify genes that mediate this communication and alter the proliferation of cells with an oncogenic Ras genotype, we carried out a tissue-specific genome-wide RNAi screen in Caenorhabditis elegans animals bearing a let-60(n1046gf) (RasG13E) allele. The screen identifies 24 genes that, when knocked down in adjacent mesodermal tissue, suppress the increased vulval epithelial cell proliferation defect associated with let-60(n1046gf). Importantly, gene knockdown reverts the mutant animals to a wild-type phenotype. Using chimeric animals, we genetically confirm that 2 of the genes function nonautonomously to revert the let-60(n1046gf) phenotype. The effect is genotype restricted, as knockdown does not alter development in a wild type (let-60(+)) or activated EGF receptor (let-23(sa62gf)) background. Although many of the genes identified encode proteins involved in essential cellular processes, including chromatin formation, ribosome function, and mitochondrial ATP metabolism, knockdown does not alter the normal development or function of targeted mesodermal tissues, indicating that the phenotype derives from specific functions performed by these cells. We show that the genes act in a manner distinct from 2 signal ligand classes (EGF and Wnt) known to influence the development of vulval epithelial cells. Altogether, the results identify genes with a novel function in mesodermal cells required for communicating with and promoting the proliferation of adjacent epithelial cells with an activated Ras genotype.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40671825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"genomicSimulation: fast R functions for stochastic simulation of breeding programs.","authors":"Kira Villiers,&nbsp;Eric Dinglasan,&nbsp;Ben J Hayes,&nbsp;Kai P Voss-Fels","doi":"10.1093/g3journal/jkac216","DOIUrl":"https://doi.org/10.1093/g3journal/jkac216","url":null,"abstract":"<p><p>Simulation tools are key to designing and optimizing breeding programs that are multiyear, high-effort endeavors. Tools that operate on real genotypes and integrate easily with other analysis software can guide users toward crossing decisions that best balance genetic gains and genetic diversity required to maintain gains in the future. Here, we present genomicSimulation, a fast and flexible tool for the stochastic simulation of crossing and selection based on real genotypes. It is fully written in C for high execution speeds, has minimal dependencies, and is available as an R package for the integration with R's broad range of analysis and visualization tools. Comparisons of a simulated recreation of a breeding program to a real data set demonstrate the simulated offspring from the tool correctly show key population features, such as genomic relationships and approximate linkage disequilibrium patterns. Both versions of genomicSimulation are freely available on GitHub: The R package version at https://github.com/vllrs/genomicSimulation/ and the C library version at https://github.com/vllrs/genomicSimulationC/.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40341760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recovering individual haplotypes and a contiguous genome assembly from pooled long-read sequencing of the diamondback moth (Lepidoptera: Plutellidae).","authors":"Samuel Whiteford,&nbsp;Arjen E Van't Hof,&nbsp;Ritesh Krishna,&nbsp;Thea Marubbi,&nbsp;Stephanie Widdison,&nbsp;Ilik J Saccheri,&nbsp;Marcus Guest,&nbsp;Neil I Morrison,&nbsp;Alistair C Darby","doi":"10.1093/g3journal/jkac210","DOIUrl":"https://doi.org/10.1093/g3journal/jkac210","url":null,"abstract":"<p><p>The assembly of divergent haplotypes using noisy long-read data presents a challenge to the reconstruction of haploid genome assemblies, due to overlapping distributions of technical sequencing error, intralocus genetic variation, and interlocus similarity within these data. Here, we present a comparative analysis of assembly algorithms representing overlap-layout-consensus, repeat graph, and de Bruijn graph methods. We examine how postprocessing strategies attempting to reduce redundant heterozygosity interact with the choice of initial assembly algorithm and ultimately produce a series of chromosome-level assemblies for an agricultural pest, the diamondback moth, Plutella xylostella (L.). We compare evaluation methods and show that BUSCO analyses may overestimate haplotig removal processing in long-read draft genomes, in comparison to a k-mer method. We discuss the trade-offs inherent in assembly algorithm and curation choices and suggest that \"best practice\" is research question dependent. We demonstrate a link between allelic divergence and allele-derived contig redundancy in final genome assemblies and document the patterns of coding and noncoding diversity between redundant sequences. We also document a link between an excess of nonsynonymous polymorphism and haplotigs that are unresolved by assembly or postassembly algorithms. Finally, we discuss how this phenomenon may have relevance for the usage of noisy long-read genome assemblies in comparative genomics.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526047/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40622671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variation in fine-scale recombination rate in temperature-evolved Drosophila melanogaster populations in response to selection.","authors":"Ari Winbush,&nbsp;Nadia D Singh","doi":"10.1093/g3journal/jkac208","DOIUrl":"https://doi.org/10.1093/g3journal/jkac208","url":null,"abstract":"<p><p>Meiotic recombination plays a critical evolutionary role in maintaining fitness in response to selective pressures due to changing environments. Variation in recombination rate has been observed amongst and between species and populations and within genomes across numerous taxa. Studies have demonstrated a link between changes in recombination rate and selection, but the extent to which fine-scale recombination rate varies between evolved populations during the evolutionary period in response to selection is under active research. Here, we utilize a set of 3 temperature-evolved Drosophila melanogaster populations that were shown to have diverged in several phenotypes, including recombination rate, based on the temperature regime in which they evolved. Using whole-genome sequencing data from these populations, we generated linkage disequilibrium-based fine-scale recombination maps for each population. With these maps, we compare recombination rates and patterns among the 3 populations and show that they have diverged at fine scales but are conserved at broader scales. We further demonstrate a correlation between recombination rates and genomic variation in the 3 populations. Lastly, we show variation in localized regions of enhanced recombination rates, termed warm spots, between the populations with these warm spots and associated genes overlapping areas previously shown to have diverged in the 3 populations due to selection. These data support the existence of recombination modifiers in these populations which are subject to selection during evolutionary change.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40607253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular mapping of quantitative trait loci for 3 husk traits using genotyping by sequencing in maize (Zea mays L.).","authors":"Jun Zhang,&nbsp;Fengqi Zhang,&nbsp;Lei Tian,&nbsp;Yong Ding,&nbsp;Jianshuang Qi,&nbsp;Hongfeng Zhang,&nbsp;Xinyuan Mu,&nbsp;Zhiyan Ma,&nbsp;Laikun Xia,&nbsp;Baojun Tang","doi":"10.1093/g3journal/jkac198","DOIUrl":"https://doi.org/10.1093/g3journal/jkac198","url":null,"abstract":"<p><p>The maize (Zea mays L.) husk consists of multiple leaf layers and plays an important role in grain growth and development. Despite significant achievements in physiological and morphological research, few studies have focused on the detection of genetic loci underlying husk-related traits due to the lack of efficient tools. In this study, we constructed an ultra-high-density linkage map using genotyping by sequencing based on a recombinant inbred line population to estimate the genetic variance and heritability of 3 husk traits, i.e. husk length, husk width, and husk layer number in 3 field environments and the combined environment. The 3 husk traits showed broad phenotypic variation and high heritability; the broad-sense heritability (H2) was 0.92, 0.84, and 0.86. Twenty quantitative trait loci were consistently detected more than 1 environment, including 9 for husk length, 6 for husk width, and 5 for husk layer number. These loci were considered as stable quantitative trait loci. Based on the quantitative trait loci mapping in the recombinant inbred line population, qHL6 and qHN4 were detected across all environments and inferred to be reliable and major-effect quantitative trait loci for husk length and husk layer number, respectively. In addition, several predicted candidate genes were identified in the region of qHL6 and qHN4, of which 17 candidate genes potentially play a role in biological processes related to development process and energy metabolism. These results will be as a useful resource for performing functional studies aimed at understanding the molecular pathways involved in husk growth and development.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40693137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"impMKT: the imputed McDonald and Kreitman test, a straightforward correction that significantly increases the evidence of positive selection of the McDonald and Kreitman test at the gene level.","authors":"Jesús Murga-Moreno,&nbsp;Marta Coronado-Zamora,&nbsp;Sònia Casillas,&nbsp;Antonio Barbadilla","doi":"10.1093/g3journal/jkac206","DOIUrl":"https://doi.org/10.1093/g3journal/jkac206","url":null,"abstract":"<p><p>The McDonald and Kreitman test is one of the most powerful and widely used methods to detect and quantify recurrent natural selection in DNA sequence data. One of its main limitations is the underestimation of positive selection due to the presence of slightly deleterious variants segregating at low frequencies. Although several approaches have been developed to overcome this limitation, most of them work on gene pooled analyses. Here, we present the imputed McDonald and Kreitman test (impMKT), a new straightforward approach for the detection of positive selection and other selection components of the distribution of fitness effects at the gene level. We compare imputed McDonald and Kreitman test with other widely used McDonald and Kreitman test approaches considering both simulated and empirical data. By applying imputed McDonald and Kreitman test to humans and Drosophila data at the gene level, we substantially increase the statistical evidence of positive selection with respect to previous approaches (e.g. by 50% and 157% compared with the McDonald and Kreitman test in Drosophila and humans, respectively). Finally, we review the minimum number of genes required to obtain a reliable estimation of the proportion of adaptive substitution (α) in gene pooled analyses by using the imputed McDonald and Kreitman test compared with other McDonald and Kreitman test implementations. Because of its simplicity and increased power to detect recurrent positive selection on genes, we propose the imputed McDonald and Kreitman test as the first straightforward approach for testing specific evolutionary hypotheses at the gene level. The software implementation and population genomics data are available at the web-server imkt.uab.cat.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9526038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40716902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Imaging-associated stress causes divergent phase transitions of RNA-binding proteins in the Caenorhabditis elegans germ line.","authors":"Mohamed T Elaswad,&nbsp;Chloe Munderloh,&nbsp;Brooklynne M Watkins,&nbsp;Katherine G Sharp,&nbsp;Elizabeth Breton,&nbsp;Jennifer A Schisa","doi":"10.1093/g3journal/jkac172","DOIUrl":"https://doi.org/10.1093/g3journal/jkac172","url":null,"abstract":"<p><p>One emerging paradigm of cellular organization of RNA and RNA-binding proteins is the formation of membraneless organelles. Examples of membraneless organelles include several types of ribonucleoprotein granules that form via phase separation. A variety of intracellular pH changes and posttranslational modifications, as well as extracellular stresses, can stimulate the condensation of proteins into granules. For example, the assembly of stress granules induced by oxidative stress, osmotic stress, and heat stress has been well characterized in a variety of somatic cell types. In the germ line, similar stress-induced condensation of proteins occurs; however, less is known about the role of phase separation during gamete production. Researchers who study phase transitions often make use of fluorescent reporters to study the dynamics of RNA-binding proteins during live cell imaging. In this report, we demonstrate that common conditions of live-imaging Caenorhabditis elegans can cause an inadvertent stress and trigger phase transitions of RNA-binding proteins. We show that this imaging-associated stress stimulates decondensation of multiple germ granule proteins and condensation of several P-body proteins. Proteins within larger ribonucleoprotein granules in meiotically arrested oocytes do not appear to be as sensitive to the stress as proteins in diakinesis oocytes of young hermaphrodites, with the exception of the germ granule protein PGL-1. Our results have important methodological implications for all researchers using live-cell imaging techniques. The data also suggest that the RNA-binding proteins within large ribonucleoprotein granules of arrested oocytes may have distinct phases, which we characterize in our companion article.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40481701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex.","authors":"Richard P Meisel,&nbsp;Danial Asgari,&nbsp;Florencia Schlamp,&nbsp;Robert L Unckless","doi":"10.1093/g3journal/jkac165","DOIUrl":"https://doi.org/10.1093/g3journal/jkac165","url":null,"abstract":"<p><p>Sex chromosomes frequently differ from the autosomes in the frequencies of genes with sexually dimorphic or tissue-specific expression. Multiple hypotheses have been put forth to explain the unique gene content of the X chromosome, including selection against male-beneficial X-linked alleles, expression limits imposed by the haploid dosage of the X in males, and interference by the dosage compensation complex on expression in males. Here, we investigate these hypotheses by examining differential gene expression in Drosophila melanogaster following several treatments that have widespread transcriptomic effects: bacterial infection, viral infection, and abiotic stress. We found that genes that are induced (upregulated) by these biotic and abiotic treatments are frequently under-represented on the X chromosome, but so are those that are repressed (downregulated) following treatment. We further show that whether a gene is bound by the dosage compensation complex in males can largely explain the paucity of both up- and downregulated genes on the X chromosome. Specifically, genes that are bound by the dosage compensation complex, or close to a dosage compensation complex high-affinity site, are unlikely to be up- or downregulated after treatment. This relationship, however, could partially be explained by a correlation between differential expression and breadth of expression across tissues. Nonetheless, our results suggest that dosage compensation complex binding, or the associated chromatin modifications, inhibit both up- and downregulation of X chromosome gene expression within specific contexts, including tissue-specific expression. We propose multiple possible mechanisms of action for the effect, including a role of Males absent on the first, a component of the dosage compensation complex, as a dampener of gene expression variance in both males and females. This effect could explain why the Drosophila X chromosome is depauperate in genes with tissue-specific or induced expression, while the mammalian X has an excess of genes with tissue-specific expression.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40566485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs.","authors":"Pleuni S Pennings,&nbsp;C Brandon Ogbunugafor,&nbsp;Ruth Hershberg","doi":"10.1093/g3journal/jkac190","DOIUrl":"https://doi.org/10.1093/g3journal/jkac190","url":null,"abstract":"<p><p>The dynamics of adaptation, reversion, and compensation have been central topics in microbial evolution, and several studies have attempted to resolve the population genetics underlying how these dynamics occur. However, questions remain regarding how certain features-the evolution of mutators and whether compensatory mutations alleviate costs fully or partially-may influence the evolutionary dynamics of compensation and reversion. In this study, we attempt to explain findings from experimental evolution by utilizing computational and theoretical approaches toward a more refined understanding of how mutation rate and the fitness effects of compensatory mutations influence adaptive dynamics. We find that high mutation rates increase the probability of reversion toward the wild type when compensation is only partial. However, the existence of even a single fully compensatory mutation is associated with a dramatically decreased probability of reversion to the wild type. These findings help to explain specific results from experimental evolution, where compensation was observed in nonmutator strains, but reversion (sometimes with compensation) was observed in mutator strains, indicating that real-world compensatory mutations are often unable to fully alleviate the costs associated with adaptation. Our findings emphasize the potential role of the supply and quality of mutations in crafting the dynamics of adaptation and reversal, with implications for theoretical population genetics and for biomedical contexts like the evolution of antibiotic resistance.</p>","PeriodicalId":520629,"journal":{"name":"G3 (Bethesda, Md.)","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2022-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9434179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40578059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}