G3: Genes|Genomes|Genetics最新文献

{"title":"Double Reduction in Allotetraploid Peanut and the Role of Chromosomal Imbalance in Unexpected Linkage Map Artifacts.","authors":"Samuele Lamon, Peter M Bourke, Brian L Abernathy, João F Dos Santos, Ignácio J de Godoy, Soraya C M Leal-Bertioli, David J Bertioli","doi":"10.1093/g3journal/jkag269","DOIUrl":"https://doi.org/10.1093/g3journal/jkag269","url":null,"abstract":"<p><p>Polyploidization in peanut (Arachis hypogaea L.) fixed heterosis but also caused a genetic bottleneck isolating cultivated peanut from its wild diploid relatives. Mechanisms such as homoeologous exchange can partially restore genetic diversity by generating new allelic combinations. Double reduction is a rare polyploid-specific segregation pattern in which a single-dosage locus yields duplex gametes. It requires multivalent formation-associated with homoeologous exchange in allopolyploids-and crossing over between non-sister chromatids. Although peanut mainly exhibits disomic pairing, occasional multivalents theoretically allow low-frequency double reduction. To estimate double reduction and examine its relationship with genetic instability, we constructed a high-density phased linkage map (9,717 markers, 0.22 cM average spacing) from a backcross population between cultivated peanut and the neoallotetraploid [A. magna × A. stenosperma]4x (MagSten). Initial maps showed distinctive double linkage group artifacts, and some progenies displayed abnormal genotyping patterns linked to unbalanced chromosomal compositions, outcomes of homoeologous exchange. Removing these progenies resolved the artifacts, revealing a previously unrecognized mapping artifact in allotetraploid peanut and suggesting a common origin for similar artifacts observed in other linkage maps. Analysis of the phased map detected double reduction in 12% of progenies; one event was confirmed as producing a genomic composition matching theoretical predictions, supporting the hypothesis that double reduction causes unbalanced genomic compositions in allopolyploids as well. These results indicate that double reduction is a rare but recurrent phenomenon in segmental allotetraploid peanut that, together with homoeologous exchange, contributes to genetic instability and generates new allelic combinations in this and likely other allopolyploid genomes.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A semi-automated genetic screen using genome-wide association analysis identifies modulators of stress-induced sleep in Caenorhabditis elegans.","authors":"Zihao John Li, Helya Honarpisheh, Sreekar Kutagulla, Kerry M LeCure, Jing Liang, David M Raizen, Christopher Fang-Yen","doi":"10.1093/g3journal/jkag266","DOIUrl":"10.1093/g3journal/jkag266","url":null,"abstract":"<p><p>Animals sleep more when they are sick. In C. elegans, stress-induced sleep (SIS) follows cellular injury such as exposure to ultraviolet (UV) light. The genetic regulators of SIS remain incompletely defined. Using robotic automation, high-throughput imaging, and genome-wide association analysis, we performed a semi-automated screen of 940 whole-genome sequenced Million Mutation Project (MMP) strains. We quantified behavioral activity and quiescence before and after ultraviolet (UV) radiation. We applied the Sequence Kernel Association Test (SKAT) to this behavioral data to prioritize a set of associated genes and observed significant enrichment of known SIS genetic regulators. Based on these results, we conducted a candidate validation screen for additional genes regulating SIS. We identified three genes (strd-1, cla-1, and egl-8), mutations in which reproducibly influence SIS. Further exploration of these genes holds potential for enhancing our understanding of the molecular basis of SIS. These findings establish a pipeline for automated behavioral phenotyping coupled with gene-based association to accelerate studies of C. elegans neurogenetics.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An atfs-1 loss-of-function screen identifies novel regulators of α-synuclein toxicity in C. elegans dopaminergic neurons.","authors":"Karolina Willicott, Joy D Iroegbu, Madeline R Greene, Aidan C Meyers, Pia Francesca Scarpino, Titus O Oyetade, Rachel Martin, Rose Davidson-Tullis, Laura A Berkowitz, Guy A Caldwell, Kim A Caldwell","doi":"10.1093/g3journal/jkag273","DOIUrl":"https://doi.org/10.1093/g3journal/jkag273","url":null,"abstract":"<p><p>Overexpression of α-synuclein (α-syn), an inherently disordered protein, triggers chronic activation of the mitochondrial unfolded protein response (UPRmt) pathway in Caenorhabditis elegans with enhanced dopaminergic (DAergic) neurodegeneration. Introduction of a loss-of-function(lf) mutation in atfs-1, the main transcriptional regulator of the UPRmt, into α-syn nematodes results in significant neuroprotection from α-syn-induced DA neuron loss. Using this sensitized neuroprotective background, we performed a F3 forward genetic screen in C. elegans atfs-1(lf) mutants to identify molecular components associated with the modulation of neurodegeneration in α-syn-expressing DA neurons. Homozygous mutant animals were examined for enhanced neurodegeneration; multiple independent alleles were uncovered. Among these, we identified new nonsense alleles encoding the histone lysine demethylases (H3K27me3) jmjd-1.2 (orthologous to human KDM7A, PHF2, and PHF8) and jmjd-3.1 (homologous to yeast CYC8). Another line carried a nonsense allele of twk-14. This gene encodes a conserved protein termed KCNK12 in mammals that facilitates passive background K+ leak currents to set and stabilize resting membrane potential. To further examine the association of these gene products in DA neurodegeneration, we used neuron-specific RNA interference, mutants, or both. DA neurodegeneration was observed in the α-syn + atfs-1(lf) background when jmjd-1.2, jmjd-3.1, or twk-14 were individually depleted. These results provide evidence that jmjd-1.2 and jmjd-3.1, which encode previously characterized H3K27me3 demethylases, and the uncharacterized twk-14 gene product, orthologous to human KCNK12, naturally confer protection from α-syn-induced neurotoxicity.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149059592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancient Truncated FtsZ Paralogs Likely Tune Cell Division in Hyphomicrobiales.","authors":"Brody Aubry, Amelia M Randich, Bailey Hudson, Elizabet Horton, Pamela J B Brown","doi":"10.1093/g3journal/jkag275","DOIUrl":"https://doi.org/10.1093/g3journal/jkag275","url":null,"abstract":"<p><p>Bacterial cell division is a well conserved, tightly regulated process that allows the separation of two viable daughter cells. In most bacteria, the proteins that drive division, termed the divisome, are recruited to mid-cell by FtsZ after it polymerizes to form the Z-ring. Interestingly, FtsZ has undergone several independent duplication events across the bacterial kingdom. In this work, we searched for FtsZ GTPase protein sequences within alphaproteobacterial genomes and observed numerous ftsZ duplications in the order Hyphomicrobiales. Hidden Markov Modeling (HMM) supported the maintenance of two distinct lineages of FtsZ GTPase duplications among three families. The Nitrobacteraceae duplication, occurring in only the genus Bradyrhizobium, exhibits a different substitution pattern from that shared by the Phyllobacteraceae and Rhizobiaceae families. Within the Rhizobiaceae lineage, Agrobacterium tumefaciens contains three paralogs of FtsZ including the essential FtsZAT, and paralogs FtsZ1, and FtsZ3. We show that FtsZ1, but not FtsZ3, inhibits cell division when expressed continuously. A hyperactive allele of ftsW partially protected against continuous expression of ftsZ1, suggesting that FtsZ1 may function to negatively regulate septal peptidoglycan biosynthesis during cell division. Overall, these observations suggest that maintenance of FtsZ paralogs in some bacteria may help control the division process.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149059659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary and Deep Learning Models Highlight Deleterious Mutations Behind the History of Sugar Beet Breeding.","authors":"Evan Long, Rajtilak Majumdar, Rachel Naegele, Kevin Dorn","doi":"10.1093/g3journal/jkag264","DOIUrl":"https://doi.org/10.1093/g3journal/jkag264","url":null,"abstract":"<p><p>Sugar beet (Beta vulgaris ssp. vulgaris) is a major global source of sucrose. Domestication and a history of breeding have shaped the distribution of deleterious mutations across the genome. Accurately resolving these variants offers a compelling avenue to accelerate crop improvement through breeding or genetic engineering. We combine three evolutionary methods to identify putatively deleterious derived mutations: angiosperm-wide DNA language deep learning model (PlantCaduceus), fine-scale evolutionary rates from Amaranthaceae plant family sequence alignments using PAML and PhyloP. We defined a high-confidence set of ∼5k deleterious variants enriched for alleles under negative selection. We then evaluate these deleterious mutations across a multi-study panel of more than 1,900 whole-genome sequenced wild and cultivated beet accessions. We found that domesticated beet accessions exhibit higher deleterious load relative to wild maritima, yet sugar beet carries significantly fewer deleterious variants than other cultivated beet crops. Historical trends show a decline in genetic load across more than a century of sugar beet entries in the U.S. NPGS, likely reflecting sustained purging during modern breeding. This combinatorial method of leveraging evolutionary conservation reveals how deleterious mutations have shaped sugar beet breeding history and provides potential targets for future selection, causal-variant discovery, and precision genome engineering.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149037328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reduced-rank random regression for improved yield prediction across the Australian wheatbelt.","authors":"Jip J C Ramakers, Martin P Boer, Jesse Hemerik, Daniela Bustos-Korts, Salvador A Gezan, Vivi Arief, Javier A Fernandez, Scott C Chapman, Fred A van Eeuwijk","doi":"10.1093/g3journal/jkag272","DOIUrl":"https://doi.org/10.1093/g3journal/jkag272","url":null,"abstract":"<p><p>Predicting complex traits like yield in new environments is challenging due to genotype-by-environment interactions (GEI). Environmental covariates (ECs) can improve prediction by describing environmental variation relevant to GEI. However, approaches that model genotype-specific responses to one or multiple ECs can become highly parameterized and difficult to fit because of the need to estimate complex covariance structures. In addition, EC-based prediction methods typically assume that future environmental conditions are known. Building on recent work, we extended a reduced-rank factor-analytic random-regression (RR) framework to enable simultaneous fitting of multiple ECs and higher-order polynomial responses. We further incorporated uncertainty in estimated reaction norms together with historical multivariate variation in ECs, addressing a realistic breeding scenario in which future EC values are unavailable. We applied the models to eight years of grain-yield data from the Australian National Variety Trials network (935 trials), spanning a wide range of environmental conditions. Using leave-one-year-out cross-validation, multi-EC RR achieved median predictive ability >20% higher than standard compound-symmetry models (CS) and up to 30% higher than single-EC RR. Extending the models to borrow information across regions further increased median predictive ability by up to four percentage points. Moreover, standard errors of prediction relative to mean yield were reduced by up to four-fold relative to models without ECs. Thus, our extended RR framework provides an effective approach for modelling GEI, delivering accurate predictions and explicit uncertainty quantification using a small set of biologically informative ECs and offering an interpretable alternative or complement to large-scale enviromic and machine-learning approaches.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149037337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA degradation by ribonuclease T2 is required for phosphate homeostasis in S. cerevisiae.","authors":"Allison M Kee, Nusrat Jahan, Davion J McFall, Cote Briggs, Lucas R Girard, Samuel Spiese, Jennifer F Garcia","doi":"10.1093/g3journal/jkag274","DOIUrl":"10.1093/g3journal/jkag274","url":null,"abstract":"<p><p>Phosphate is a critical building block for key biomolecules including ATP, DNA, RNA, and phospholipids. Consequently, cells monitor phosphate levels and acquire phosphate when intracellular levels become low. Here we demonstrate an unanticipated connection between the enzymatic activity of the S. cerevisiae RNase T2 ortholog, Rny1, and phosphate availability. Rny1 has been studied for its role in autophagy-linked RNA degradation under starvation conditions. Here we find that in nutrient-rich conditions, cells lacking Rny1 function exhibit phosphate starvation phenotypes and aberrantly activate the PHO signaling pathway despite the presence of high levels of inorganic phosphate in the growth media. This activation is evidenced by increased PHO gene transcript levels and increased nuclear localization of Pho4 in rny1Δ strains. Complementation of rny1Δ with wild-type RNY1 and human RNase T2 restores PHO transcript levels to those typically observed in exponentially growing cells. This implicates RNase T2-dependent RNA degradation as required for maintaining intracellular phosphate levels, even under phosphate-rich conditions. Furthermore, consistent with its potential role in freeing phosphate from degraded RNA, RNY1 expression is itself induced under phosphate-limited conditions. These observations suggest that RNase T2-mediated RNA decay is a part of a potentially conserved metabolic recycling pathway that provides available phosphate from degraded RNA to growing cells. These findings reframe RNA as a key metabolic resource and positions RNase T2 enzymes, and their function in RNA degradation, as an unexpected player in phosphate homeostasis.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149037290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pheromone circuits and transcriptional cascades modulating transcriptional and chromatin states in the Drosophila central brain with social experience.","authors":"Chengcheng Du, Jesús Emiliano Sotelo Fonseca, Lanling Jia, Shayna Scott, Sumie Okuwa, Sare Koruk, Corbin D Jones, Pelin C Volkan","doi":"10.1093/g3journal/jkag263","DOIUrl":"10.1093/g3journal/jkag263","url":null,"abstract":"<p><p>Social experience significantly influences the behavioral and physiological responses of animals, including humans. In many animals, social isolation increases aggression, courtship, locomotion, and feeding while disrupting sleep. This occurs when peripheral neurons detect social signals, such as pheromones, which activate brain circuits involved in decision-making. However, the molecular and circuit mechanisms of how chronic social isolation or enrichment alter gene expression and affect neuronal function and behavior remain unclear. In this study, we examined how transcription patterns and chromatin marks in male Drosophila brains change in response to social experience, and the effect of pheromone receptors and transcription factors involved in social experience-dependent changes in behaviors. We focused on pheromone receptors Or47b and Or67d, as well as transcription factors FruM and DsxM. Our findings suggest that social experience affects multiple genes in the central brain. Disrupting Or47b, Or67d, FruM, and DsxM function moderated the transcriptional responses through antagonistic interactions. Specifically, Or47b showed a primary association with transcriptional responses to social isolation in conjunction with DsxM function, while Or67d and FruM were linked to the regulation of responses to group housing. Notably, fruM and dsxM mutants exhibited more extensive transcriptional changes in the brain than Or mutants, particularly in FruM/DsxM target genes. While social experience did not lead to detectable alterations in the overall chromatin profile across the whole brain, mutants of the four genes showed significant changes in the enrichment of H3K4me3 and RNA polymerase II (RNAPolII) compared to wild type. Furthermore, mutants in fruM and dsxM generally eliminated social experience-dependent changes in sleep and locomotion behaviors, whereas Or mutants exhibited more modest disruptions. Overall, our results uncover the pheromone circuits and transcriptional cascades in regulating molecular and behavioral responses to social experience.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149037313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A method to screen for meiotic drive using embryonic markers.","authors":"Benjamin K McCormick, Daniel A Barbash","doi":"10.1093/g3journal/jkag242","DOIUrl":"10.1093/g3journal/jkag242","url":null,"abstract":"<p><p>Meiotic drivers are selfish elements that co-opt gametogenesis to increase their own transmission. Driving alleles may spread in a population even if harmful to overall fitness, requiring the emergence of host suppressors to ameliorate these costs. In some cases, intense coevolutionary arms races between drivers and their host genomes may occur. These conflicts have been invoked to explain the rapid evolution of karyotypes and reproduction-associated proteins across the tree of life. Despite their evolutionary importance, relatively few meiotic drivers have been well-characterized, in large part due to the difficulties inherent to detecting meiotic drivers, distinguishing them from viability effects, and performing systematic screens. To address these gaps, we present an approach to driver detection at the embryo stage in wild-derived Drosophila melanogaster. By combining fluorescent markers with a method to induce embryonic arrest at a standard developmental stage, we detect transmission of wild-derived alleles as compared to their fluorescently marked homologs in early embryos, before most fitness differences among alleles (which may mimic drive) manifest. We provide proof-of-concept for the approach and identify several areas for future improvement.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Telomere-to-telomere co-mapping of transposable elements and human genes identifies a cluster of young L1 elements in the interferon-alpha domain with potential evolutionary arms-race.","authors":"Daniil Nikitin","doi":"10.1093/g3journal/jkag250","DOIUrl":"https://doi.org/10.1093/g3journal/jkag250","url":null,"abstract":"<p><p>Transposable elements (TEs) have played a central role in major evolutionary transitions across the human lineage, from eukaryogenesis to the emergence of the eutherian placenta, and are currently reactivated in cancer and autoimmune diseases. The complete telomere-to-telomere (T2T) assembly enables comprehensive investigation of TE contributions to gene regulation. Using a 10 kb window around transcription start sites, we mapped 3,709,429 human TEs to 28,738 genes against a 500-permutation background and assessed the enrichment and functional associations of 6 TE classes and 44 families. We identified a 220 kb interferon-alpha domain enriched with young L1 elements: 77 of its 175 TEs are evolutionary young L1 copies from 36 subfamilies, at mean divergence 135.7 against 188.2 genome-wide. This is consistent with recent L1 activity and could indicate a recent evolutionary arms-race affecting innate immune gene regulation. Distinct TE classes exhibited specific functional associations: SVA elements were enriched near genes involved in transcription termination; Alu elements were linked to RNA processing and splicing; MIR elements were associated with zinc homeostasis and voltage-gated potassium channel genes; LINE elements were enriched near genes related to lipid metabolism and olfactory perception; and LTR elements were associated with ion transport. This correlative map provides a positional baseline against which epigenomic and functional TE studies can be normalized, and a set of candidate loci for further investigation of evolutionary arms race.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}