GeneticsPub Date : 2025-08-27DOI: 10.1093/genetics/iyaf170
Erich M Schwarz, Anil Baniya, Jennifer K Heppert, Hillel T Schwartz, Chieh-Hsiang Tan, Igor Antoshechkin, Paul W Sternberg, Heidi Goodrich-Blair, Adler R Dillman
{"title":"Genomes of the entomopathogenic nematode Steinernema hermaphroditum and its associated bacteria.","authors":"Erich M Schwarz, Anil Baniya, Jennifer K Heppert, Hillel T Schwartz, Chieh-Hsiang Tan, Igor Antoshechkin, Paul W Sternberg, Heidi Goodrich-Blair, Adler R Dillman","doi":"10.1093/genetics/iyaf170","DOIUrl":"10.1093/genetics/iyaf170","url":null,"abstract":"<p><p>As an entomopathogenic nematode (EPN), Steinernema hermaphroditum parasitizes insect hosts and harbors symbiotic Xenorhabdus griffinae bacteria. In contrast to other Steinernematids, S. hermaphroditum has hermaphroditic genetics, offering the experimental scope found in Caenorhabditis elegans. To enable study of S. hermaphroditum, we have assembled and analyzed its reference genome. This genome assembly has five chromosomal scaffolds and 83 unassigned scaffolds totaling 90.7 Mb, with 19,426 protein-coding genes having a BUSCO completeness of 88.0%. Its autosomes show higher densities of strongly conserved genes in their centers, as in C. elegans, but repetitive elements are evenly distributed along all chromosomes, rather than with higher arm densities as in C. elegans. Either when comparing protein motif frequencies between nematode species or when analyzing gene family expansions during nematode evolution, we observed two categories of genes preferentially associated with the origin of Steinernema or S. hermaphroditum: orthologs of venom genes in S. carpocapsae or S. feltiae; and some types of chemosensory G protein-coupled receptors, despite the tendency of parasitic nematodes to have reduced numbers of chemosensory genes. Three-quarters of venom orthologs occurred in gene clusters, with the larger clusters comprising functionally diverse gene groups rather than paralogous repeats of a single venom gene. While assembling S. hermaphroditum, we coassembled bacterial genomes, finding sequence data for not only the known symbiont, X. griffinae, but also for eight other bacterial genera. All eight genera have previously been observed to be associated with Steinernema species or the EPN Heterorhabditis, and may constitute a \"second bacterial circle\" of EPNs.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975504","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}
GeneticsPub Date : 2025-08-26DOI: 10.1093/genetics/iyaf160
Carolin C Wendling, Zachary M Bailey
{"title":"Pioneer of bacterial genetics: the legacy of Esther Miriam Lederberg.","authors":"Carolin C Wendling, Zachary M Bailey","doi":"10.1093/genetics/iyaf160","DOIUrl":"https://doi.org/10.1093/genetics/iyaf160","url":null,"abstract":"<p><p>Esther Miriam Lederberg's brilliant scientific lifework, from the discovery of phage lambda, bacterial conjugation, and replica plating, provided essential tools that have been shaping the field of bacterial genetics for decades. Fundamental principles and ideas derived from her work have influenced many significant discoveries in microbial genetics over the past 70 years. From the operon model to recombinant DNA technology, from antibiotic resistance research to the discovery of restriction enzymes, Esther's work has set the stage for groundbreaking scientific work including many Nobel Prizes. Despite her discoveries, her contributions were often overlooked, and recognition was often given to her collaborators, particularly her husband. Thus, beyond her scientific impact, her perseverance and her ability to circumvent societal conventions are among her most important legacies that have been paving the way for future generations of scientists. In this article, we honor Esther Lederberg by revisiting her scientific discoveries, exploring how they influenced our current understanding of molecular genetics, and reflecting on the broader importance of recognizing and rewarding equity in the scientific community.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975467","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}
GeneticsPub Date : 2025-08-22DOI: 10.1093/genetics/iyaf169
Parul Johri, Brian Charlesworth
{"title":"A gene-based model of fitness and its implications for genetic variation: Genetic and inbreeding loads.","authors":"Parul Johri, Brian Charlesworth","doi":"10.1093/genetics/iyaf169","DOIUrl":"https://doi.org/10.1093/genetics/iyaf169","url":null,"abstract":"<p><p>In the companion paper to this, we examined the consequences for patterns of linkage disequilibrium of the \"gene\" model of fitness, which postulates that the effects of recessive or partially recessive deleterious mutations located at different sites within a gene fail to complement each other. Here, we examine the consequences of the gene model for the genetic and inbreeding loads, using both analytical and simulation methods, and contrast it with the frequently used \"sites\" model that allows allelic complementation. We show that the gene model results in a slightly lower genetic load, but a much smaller inbreeding load, than the sites model, implying that standard predictions of mutational contributions to inbreeding depression may be overestimates. Synergistic epistasis between pairs of mutations was also modeled, and shown to considerably reduce the inbreeding load for both the gene and sites models. The theoretical results are discussed in relation to data on inbreeding load in Drosophila melanogaster. The widespread assumption that inbreeding depression is largely due to deleterious mutations should be re-examined in the light of our findings.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975533","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}
GeneticsPub Date : 2025-08-22DOI: 10.1093/genetics/iyaf174
David Tadres, Hiroshi M Shiozaki, Ibrahim Tastekin, David L Stern, Matthieu Louis
{"title":"An essential experimental control for functional connectivity mapping with optogenetics.","authors":"David Tadres, Hiroshi M Shiozaki, Ibrahim Tastekin, David L Stern, Matthieu Louis","doi":"10.1093/genetics/iyaf174","DOIUrl":"https://doi.org/10.1093/genetics/iyaf174","url":null,"abstract":"<p><p>To establish functional connectivity between two candidate neurons that might form a circuit element, a common approach is to activate an optogenetic tool such as Chrimson in the candidate pre-synaptic neuron and monitor fluorescence of the calcium-sensitive indicator GCaMP in a candidate post-synaptic neuron. While performing such experiments in Drosophila, we found that low levels of leaky Chrimson expression can lead to strong artifactual GCaMP signals in presumptive postsynaptic neurons even when Chrimson is not intentionally expressed in any particular neurons. Withholding all-trans retinal, the chromophore required as a co-factor for Chrimson response to light, eliminates GCaMP signal but does not provide an experimental control for leaky Chrimson expression. Leaky Chrimson expression appears to be an inherent feature of current Chrimson transgenes, since artifactual connectivity was detected with Chrimson transgenes integrated into multiple genomic locations. While these false-positive signals may complicate the interpretation of functional connectivity experiments, we illustrate how a no-Gal4 negative control improves interpretability of functional connectivity assays. We also propose a simple but effective procedure to identify experimental conditions that minimize potentially incorrect interpretations caused by leaky Chrimson expression.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975480","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}
GeneticsPub Date : 2025-08-22DOI: 10.1093/genetics/iyaf168
Parul Johri, Brian Charlesworth
{"title":"A gene-based model of fitness and its implications for genetic variation: Linkage disequilibrium.","authors":"Parul Johri, Brian Charlesworth","doi":"10.1093/genetics/iyaf168","DOIUrl":"https://doi.org/10.1093/genetics/iyaf168","url":null,"abstract":"<p><p>A widely used model of the effects of mutations on fitness (the \"sites\" model) assumes that heterozygous recessive or partially recessive deleterious mutations at different sites in a gene complement each other, similarly to mutations in different genes. However, the general lack of complementation between major effect allelic mutations suggests an alternative possibility, which we term the \"gene\" model. This model assumes that a pair of heterozygous deleterious mutations in trans behave effectively as homozygotes, so that the fitnesses of trans heterozygotes are lower than those of cis heterozygotes. We examine the properties of the two different models, using both analytical and simulation methods. We show that the gene model predicts positive linkage disequilibrium (LD) between deleterious variants within the coding sequence under conditions when the sites model predicts zero or slightly negative LD. We also show that focussing on rare variants when examining patterns of LD, especially with Lewontin's D´ measure, is likely to produce misleading results with respect to inferences concerning the causes of the sign of LD. Synergistic epistasis between pairs of mutations was also modeled; it is less likely to produce negative LD under the gene model than the sites model. The theoretical results are discussed in relation to patterns of LD in natural populations of several species.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975506","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}
GeneticsPub Date : 2025-08-22DOI: 10.1093/genetics/iyaf176
Rebeca Carballar-Lejarazú, Thai Binh Pham, Taylor Tushar, Anthony A James
{"title":"Mutant allele formation and inheritance during Cas9/guide RNA-mediated gene drive in a population modification mosquito strain for human malaria control.","authors":"Rebeca Carballar-Lejarazú, Thai Binh Pham, Taylor Tushar, Anthony A James","doi":"10.1093/genetics/iyaf176","DOIUrl":"https://doi.org/10.1093/genetics/iyaf176","url":null,"abstract":"<p><p>Gene-drive systems are under development for population modification of anopheline vectors of human malaria parasites. Key to their success is the fixation in target mosquito populations of genes encoding molecules that prevent parasite transmission. High-efficiency Cas9/guide RNA (gRNA)-based gene-drive systems can facilitate this objective. A potential challenge to these systems is the presence of naturally-occurring or drive system-induced sequence polymorphisms in the genomic target site that could impede Cas9/gRNA-mediated cleavage and negatively impact gene-drive dynamics and fixation. Careful choice of the target site can mitigate the impact of natural variation, and here we analyze drive system-mediated, target-site mutagenesis in the outcross and testcross progeny of an Anopheles gambiae strain homo- and hemizygous for the TP13-based gene-drive system. The resulting data allow estimates of the rates at which drive-system activity generates mutant target-site alleles in the germline and the impact of inherited paternal- and maternal-effect mutations. Functional and non-functional mutant alleles are recovered from the germlines at average rates per target gene/generation of 0.08% for paternal and 0.33% for maternal testcross lineages with an overall average rate of 0.21%. Clustering effects amplify the potential inheritance frequencies of the mutant alleles. Mutations originating in the germlines represent 47% of the total inherited in testcross progeny with the balance coming from mutant alleles generated by paternal and maternal effects inherited through the respective parental lineages. This approach allows estimating potential cleavage-resistant allele formation and inheritance for this drive system in this species and provides empirically-derived values to inform more realistic data-driven, gene-drive modeling.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975511","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}
GeneticsPub Date : 2025-08-21DOI: 10.1093/genetics/iyaf165
Mara J W Schwiesow, Leah A Farinella, Marina Ruzic, Jake T Leinas, Nels C Elde, Zoë A Hilbert
{"title":"Distinct routes to thermotolerance in the fungal pathogen Cryptococcus neoformans.","authors":"Mara J W Schwiesow, Leah A Farinella, Marina Ruzic, Jake T Leinas, Nels C Elde, Zoë A Hilbert","doi":"10.1093/genetics/iyaf165","DOIUrl":"https://doi.org/10.1093/genetics/iyaf165","url":null,"abstract":"<p><p>Increasing temperatures associated with climate change have the potential for far-reaching impacts on human health and disease vectors, including fungal pathogens. Pathogenic fungi occupy a wide range of environments across the world, and their ranges have been slowly expanding in recent decades due, in part, to climate change. Despite these links between increasing temperature and higher prevalence of fungal disease, the direct effects of rising environmental temperatures on the evolution of pathogenic fungi remains unclear. In this study, we investigated how increasing temperatures drive adaptive evolution in the human fungal pathogen Cryptococcus neoformans. First, we performed serial passages of a C. neoformans environmental isolate with gradual changes in temperature over the course of 38 days. Through this approach we identified several distinct thermally adapted isolates with competitive growth advantages over the parental strain at high temperatures. We then characterized the phenotypic and genetic changes acquired in these evolved isolates, which include alteration of cell size, colony morphology, and, notably, antifungal resistance. Our genetic analyses further revealed distinct genes that facilitate thermoadaptation in different populations-identifying new molecular players in the regulation of this trait and revealing that there are multiple independent routes to gaining thermotolerance. These results highlight the remarkable flexibility of fungi to adapt rapidly to new environments and raise pressing questions about the impacts of rising environmental temperatures on the future of infectious diseases and human health.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975448","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}
GeneticsPub Date : 2025-08-21DOI: 10.1093/genetics/iyaf173
Katherine M Hanson, Anthony D Long, Stuart J Macdonald
{"title":"Extreme QTL mapping enables the identification of novel zinc toxicity response loci in Drosophila melanogaster.","authors":"Katherine M Hanson, Anthony D Long, Stuart J Macdonald","doi":"10.1093/genetics/iyaf173","DOIUrl":"https://doi.org/10.1093/genetics/iyaf173","url":null,"abstract":"<p><p>Heavy metals are a widespread environmental contaminant, and even low levels of some metals can disrupt cellular processes and result in DNA damage. However, the consequences of metal exposure are variable among individuals, with susceptibility to metal toxicity representing a complex trait influenced by genetic and non-genetic factors. To uncover toxicity response genes, and better understand responses to metal toxicity, we sought to dissect resistance to zinc, a metal required for normal cellular function, which can be toxic at high doses. To facilitate efficient, powerful discovery of Quantitative Trait Loci (QTL) we employed extreme, or X-QTL mapping, leveraging a multiparental, recombinant Drosophila melanogaster population. Our approach involved bulk selection of zinc-resistant females, sequencing several replicate pools of selected and control animals, and identified QTL as genomic positions showing consistent allele frequency shifts between treatments. We successfully identified seven regions segregating for resistance/susceptibility alleles and implicated several strong candidate genes. Phenotypic characterization of populations derived from selected or control animals revealed that our selection procedure resulted in greater egg-to-adult emergence, and a reduced developmental delay on zinc media. We subsequently measured emergence and development time for a series of midgut-specific RNAi gene knockdowns and genetic controls raised in both zinc-supplemented and normal media. This identified ten genes with significant genotype-by-treatment effects, including pHCl-2, which encodes a zinc sensor protein. Our work highlights recognized and novel contributors to zinc toxicity resistance in flies, and provides a pathway to a broader understanding of the biological impact of metal toxicity.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144975464","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}
GeneticsPub Date : 2025-08-21DOI: 10.1093/genetics/iyaf175
Gemma Puixeu, Laura Katherine Hayward
{"title":"The relationship between sexual dimorphism and intersex correlation: do models support intuition?","authors":"Gemma Puixeu, Laura Katherine Hayward","doi":"10.1093/genetics/iyaf175","DOIUrl":"https://doi.org/10.1093/genetics/iyaf175","url":null,"abstract":"<p><p>The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by shared genetic architecture between the sexes. Indeed, it is commonly expected that SD should negatively correlate with the intersex correlation (the genetic correlation between effects of segregating variants in females and males, r fm), either because (1) traits with ancestrally low r fm are less constrained in their ability to respond to sex-specific selection and thus evolve to be more dimorphic, or because (2) sex-specific selection, driving sexual dimorphism evolution, also acts to reduce r fm. Despite the intuitive appeal and prominence of these ideas, their generality and the conditions in which they hold remain unclear. Here, we develop models incorporating sex-specific stabilizing selection, mutation and genetic drift to examine the relationship between r fm and SD. We show that the two commonly-discussed mechanisms with the potential to generate a negative correlation between SD and r fm could just as easily generate a positive association, since the standard line of reasoning hinges on a hidden assumption that sex-specific adaptation more frequently favors increased dimorphism than reduced dimorphism. Our results provide, to our knowledge, the first mechanistic framework for understanding the conditions under which a correlation between r fm and SD may arise and offer a compelling explanation for inconsistent empirical evidence. We also make the intriguing observation that-even when selection between the two sexes is identical-drift generates nonzero SD. We quantify this effect and discuss its significance.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144974961","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}
GeneticsPub Date : 2025-08-19DOI: 10.1093/genetics/iyaf166
Katherine Spilsbury, Jing Wu, Michael Reidy, Peter A Kropp
{"title":"The mitochondrial trans-2-enoyl-coA reductase is necessary for mitochondrial homeostasis in C. elegans.","authors":"Katherine Spilsbury, Jing Wu, Michael Reidy, Peter A Kropp","doi":"10.1093/genetics/iyaf166","DOIUrl":"10.1093/genetics/iyaf166","url":null,"abstract":"<p><p>Fatty acids function not only as signaling molecules and for energy storage, but also as essential cofactors for mitochondrial enzymes. These fatty acid cofactors are produced by the mitochondrial fatty acid synthesis pathway (mtFAS), the terminal enzyme of which is mitochondrial trans-2-enoyl-coA reductase (MECR). Dysfunction of MECR prevents the synthesis of fatty acids and is the monogenic cause of MEPAN syndrome, a rare mitochondrial disease characterized by dystonia, basal ganglia degeneration, and optic nerve atrophy. Given the necessity of mtFAS products for mitochondrial function, MECR should be essential. Yet, evidence from MEPAN individuals and model organisms with MECR loss of function indicate that mitochondrial function is not as severely impaired as would be expected. However, many of these studies have been limited to single cells or cell types. To better understand the role of MECR and its products in a multicellular system, we used CRISPR/Cas9 to knock out its two orthologs in C. elegans, MECR-1 and MECR-2. We found that only MECR-1 is necessary for normal mitochondrial function, germline development, and neuromuscular function. We thus establish a model in which further studies of MECR/MECR-1 can clarify its biochemical, developmental, and physiological roles.</p>","PeriodicalId":48925,"journal":{"name":"Genetics","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876358","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}