G3: Genes|Genomes|Genetics最新文献

{"title":"Transcriptomic profiles of the maternal-to-zygotic transition for Drosophila embryos exposed to acute and chronic heat stress.","authors":"Faizan Rashid, Natalie Biel, Jenny Drnevich, Anna Marie Sokac","doi":"10.1093/g3journal/jkag203","DOIUrl":"10.1093/g3journal/jkag203","url":null,"abstract":"<p><p>Heat stress challenges embryo survival, but the molecular reasons for this are unclear. We investigated how heat stress alters the maternal-to-zygotic transition (MZT) during Drosophila melanogaster development. Using RNA sequencing, we characterized the MZT under nonstress, acute, and chronic heat stress conditions. MZT genes were defined as those differentially expressed between the minor and major waves of zygotic genome activation. MZT genes were associated with multiple processes, including transcription, splicing, translation, and development. Under acute stress, the MZT deviated little from nonstressed embryos except that heat shock protein (HSP) genes were activated, and maternal transcript clearance was minimally misregulated. Under chronic stress, a core MZT persisted; but stress-related gene expression was obvious, maternal transcripts were strongly misregulated, and embryos showed poor survival. Overall, the MZT is robust, but increasingly falters with more severe stress. We present our dataset as a resource to aid molecular understanding of embryo resilience and vulnerability to environmental stressors.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148720295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic indicators of gene function: a systematic assessment of the human genome.","authors":"Helena B Cooper, Karla E Rojas López, Daniela Schiavinato, Michael A Black, Paul P Gardner","doi":"10.1093/g3journal/jkag215","DOIUrl":"10.1093/g3journal/jkag215","url":null,"abstract":"<p><p>Proteins and non-coding RNAs are functional products of the genome that are central for crucial cellular processes. With recent technological advances, researchers can sequence genomes in the thousands and probe numerous genomic activities of many species and conditions. Such studies have identified thousands of potential proteins, RNAs, and associated activities. However, there are conflicting interpretations of the results and therefore which regions of the genome are \"functional.\" Here we investigate the relative strengths of associations between coding and non-coding gene functionality and genomic features, by comparing reliably annotated functional genes to nongenic regions of the genome. We find that the strongest and most consistent associations between functional genes and genomic features are transcriptional activity and evolutionary conservation. We also evaluated sequence-based statistics, genomic repeats, and epigenetic and population variation data. Other features strongly associated with function include histone marks, chromatin accessibility, genomic copy number, and sequence alignment statistics such as coding potential and covariation. We also identify potential issues with SNP annotations in short non-coding RNAs, as some highly conserved ncRNAs have significantly higher than expected SNP densities. Our results demonstrate the importance of evolutionary conservation and transcription activity for indicating protein-coding and non-coding gene function. Both should be taken into consideration when differentiating between functional sequences and biological or experimental noise.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148790536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Splicing genes as main targets of differential splicing.","authors":"Torstein Tengs, Thomas LaFramboise, Yossef Baidi, Rameen Beroukhim, Won-Young Choi, Hyo Young Choi, David Neil Hayes","doi":"10.1093/g3journal/jkag213","DOIUrl":"10.1093/g3journal/jkag213","url":null,"abstract":"<p><p>Splicing of transcripts via the spliceosome machinery is a complex process involving a multitude of proteins and short noncoding RNAs. In addition to full-length transcripts with all exons in the genomically encoded order, alternatively spliced transcripts can also be produced through alternative splicing of pre-mRNA. We have attempted to identify which genes are most frequently targeted by differential splicing using both downloaded and original RNA-Seq data from several species and tissue types. In order to identify splicing variation on an individual-to-individual basis, random contrasting of samples within compatible sets of samples was done. Both when analyzing sequence data from similar source material (same tissue from individuals kept under similar conditions) and when contrasting samples that are more different, such as different tissue types, genes associated with the splicing process itself seem to be the most recurring targets.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148764422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing CRISPR/Cas9 mutagenesis in Drosophila dendritic arborization neurons to avoid cytotoxicity.","authors":"Vinicius N Duarte, Viana Najafi, Katherine L Thompson-Peer","doi":"10.1093/g3journal/jkag211","DOIUrl":"10.1093/g3journal/jkag211","url":null,"abstract":"<p><p>Genetic perturbations are one of the great strengths of the model organism Drosophila melanogaster, with approaches such as classical mutagenesis and RNA interference enabling a wealth of biological discoveries. A more recent approach for altering gene expression is CRISPR/Cas9-based mutagenesis. As with any new tool, however, its use must be optimized. High expression of Cas9 has been shown to cause cytotoxicity in some cell types, including class IV dendritic arborization (da) neurons. In this study, we provide evidence that Cas9 expression causes cytotoxicity in class I da neurons, in addition to class IV da neurons, both of which are widely used to study neuronal development and regeneration. We then systematically evaluated available Cas9 transgenes designed to titrate Cas9 expression, called uCas9 transgenes. We show that the expression of these uCas9 transgenes results in little to no cytotoxicity in various classes of da neurons. Immunostaining revealed drastic reductions in Cas9 protein levels for da neurons expressing the uCas9(L) transgene. Lastly, we demonstrate that the uCas9(L) transgene effectively and specifically gene edits in both class I and class IV da neurons, lowering the expression of GFP-tagged proteins and producing loss-of-function morphological phenotypes when targeting endogenous loci. Thus, we refine the use of CRISPR mutagenesis in Drosophila da neurons through titration of Gal4/UAS-mediated Cas9 expression using existing uCas9 transgenes, a feasible and flexible approach that may be useful for other labs encountering Cas9 cytotoxicity in their own model systems.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Drosophila beanbag (beba) encodes an insect receptor tyrosine kinase associated with reproductive niche organization.","authors":"Sarah Mele, Sarah Bright, Emily Kerton, Travis K Johnson","doi":"10.1093/g3journal/jkag227","DOIUrl":"10.1093/g3journal/jkag227","url":null,"abstract":"<p><p>Receptor tyrosine kinases (RTKs) are cell surface proteins that govern many critical cell fate decisions and their dysregulation is a major cause of diseases such as cancer. Much of what we know about how these proteins work in cells and tissues comes from model organisms such as the fruit fly Drosophila. Here, we identify and provide an initial characterization of a previously unstudied Drosophila receptor tyrosine kinase encoded by CG3277, which we name beanbag (beba). Ectopic beba expression was associated with increased phosphor-Akt and diphospho-ERK signals and produced gain-of-function phenotypes resembling those caused by other Drosophila RTKs. Using a MiMIC-derived T2A-GAL4 allele, we show that Drosophila beba is expressed in digestive, nervous, and reproductive systems, in locations suggestive of potential roles in endoreplication and/or stem cell niche support. Animals transheterozygous for beba loss-of-function alleles were viable, developed at a normal rate, and showed no detectable change in enterocyte DNA content under standard conditions. However, beba loss-of-function females had fewer ovarioles, consistent with a role in the ovarian terminal filament, and males had increased testis hub nuclei number and hub volume, suggesting beba may regulate somatic niche architecture in the Drosophila gonad. Phylogenetic analysis places Beba within a Ret/Tor-related RTK radiation and supports the existence of a distinct Beba family in insects. Together, these data support the classification of Beba as a lineage-restricted Drosophila RTK and implicate it in reproductive niche organization.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148790006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conserved sex-biased DNA methylation patterns target key developmental genes and reproductive function in two Poeciliidae species.","authors":"David C H Metzger, Judith E Mank","doi":"10.1093/g3journal/jkag228","DOIUrl":"10.1093/g3journal/jkag228","url":null,"abstract":"<p><p>Sexual dimorphism provides a powerful framework for studying how regulatory mechanisms generate phenotypic divergence from a shared genome. Many sex-specific traits arise from differences in gene expression, which can be mediated by epigenetic mechanisms such as DNA methylation. These mechanisms contribute to the organization of gene regulatory variation across tissues, genes, and chromosomes, with potential consequences for the emergence and maintenance of sexually dimorphic phenotypes. Using a comparative epigenomic approach we investigate sex-biased DNA methylation in gonad and muscle tissue across 2 closely related Poeciliidae species, Poecilia reticulata and Poecilia wingei. We address 3 questions: (i) how conserved are sex-biased DNA methylation patterns across species and tissues; (ii) are conserved sex-biased methylation patterns associated with genes involved in developmental and transcriptional regulation; and (iii) are sex-biased epigenetic patterns enriched on the sex chromosome? We identify extensive conservation of sex-biased differentially methylated regions in gonadal tissue, with strong cross-species concordance, whereas muscle shows little conservation of sex-specific differential methylation. Conserved male-hypomethylated regions are enriched near genes involved in developmental transcriptional regulation and gonadal differentiation. Methylation-expression coupling distinguishes sex-biased reproductive gene functions, with male-biased genes enriched for spermatogenesis and motility and female-biased genes enriched for sperm-egg interaction processes. Sex-biased DNA methylation is broadly distributed across the genome, with localized regulatory regions on the sex chromosome. Together, these results show that conserved sex-biased DNA methylation is highly tissue-specific and associated with reproductive regulatory function, supporting a model in which gonadal epigenetic architecture reflects conserved regulatory organization underlying sexual dimorphism.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148790635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multiplex droplet digital PCR assay for chromosome copy-number determination in Candida albicans.","authors":"Eli Isael Maciel, Sylvain Ursuegui, Sana Ahmed-Seghir, Corinne Maufrais, Stéphanie Roy, Cécile Gautier, Philipp Brandt, Cécile Jovelet, Laras Pitayu, Iuliana V Ene","doi":"10.1093/g3journal/jkag201","DOIUrl":"10.1093/g3journal/jkag201","url":null,"abstract":"<p><p>Chromosome copy-number variation is a major contributor to genome plasticity and adaptation in Candida albicans, a leading fungal pathogen of humans. Aneuploidy, defined as deviations from the normal diploid chromosome set, rapidly alters gene dosage and is often observed during exposure to host-imposed and antifungal stress. Accurate detection and quantification of chromosomal copy-number changes are thus essential to dissect the mechanisms by which C. albicans adapts and evolves. Here, we describe the development, optimization, and validation of a 6-color, 16-plex droplet digital PCR assay for simultaneous quantification of all C. albicans chromosome arms in a single reaction. Each target is detected by a unique dual-color or single-color combination of probes, enabling high-order multiplexing through binary fluorescence encoding. Following optimization of probe concentrations, PCR cycling parameters, genomic DNA extraction, and pretreatment with restriction enzymes, the assay provides accurate, reproducible chromosome-level copy-number estimates that correlate closely with whole-genome sequencing results across euploid and aneuploid isolates. Compared to whole-genome sequencing, the assay is rapid, cost-effective, and scalable, requiring minimal DNA input and allowing high-throughput analysis of large collections of isolates. The 16-plex assay thus provides a platform for dissecting genome instability and adaptive evolution in C. albicans.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148601161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic variation in a plant-parasitic nematode is associated with host gene expression changes conserved across evolutionarily distant host plants.","authors":"Dahlia M Nielsen","doi":"10.1093/g3journal/jkag204","DOIUrl":"10.1093/g3journal/jkag204","url":null,"abstract":"<p><p>A hallmark of the interactions between endoparasites (parasites that live within plant tissue) and their hosts is the parasites' ability to hijack host gene expression to support their own existence. While a number of studies have been performed to identify plant genes that are recruited in this manner, there is much that remains unknown. One mechanism by which this behavior can be explored is by using a traditional genetics approach: identifying connections between genetic variation and phenotype variation. To that end, we leverage experiments examining tissue from 3 host plant species, infected with one of 2 genetically distinct strains of the endoparasite Meloidogyne hapla. Using RNA-Seq data, we identify plant gene expression patterns that differ according to the genetic background of the infecting parasite. We also show that parasite genotype-host expression phenotype associations are consistent across plant species. These results indicate that the plant genes recruited by the parasite are influenced by the parasite's genetic background and that these differential choices are conserved across evolutionarily distant hosts. We also leverage public data to identify conserved host expression differences when comparing M. hapla-infected plants to uninfected plants. Finally, we demonstrate that parasite gene expression varies according to the parasite's genetic background and show that these signals are also conserved under different host species.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148591161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A population genomic resource for Drosophila pseudoobscura.","authors":"Yesbol Manat, Zhao Zheng, Camryn A Kritzell, Christopher A Gonzales, Richard P Meisel","doi":"10.1093/g3journal/jkag210","DOIUrl":"10.1093/g3journal/jkag210","url":null,"abstract":"<p><p>Drosophila pseudoobscura is an historically important organism in evolutionary genetics, serving as a model system in studies of chromosomal inversions, speciation, sex chromosome evolution, and sex-ratio drive. However, previous population genetics analysis of D. pseudoobscura focused on individual chromosomes or used fragmented genome assemblies as a reference. To address these shortcomings, we generated a D. pseudoobscura population genomics resource consisting of newly sequenced genomes from 60 inbred lines sampled across the species' geographic range in North America. Using these data and a chromosome-scale reference genome, we examined patterns of nucleotide diversity and population structure across the chromosomes. We found no strong evidence of population structure on most chromosomes, consistent with prior results. In contrast, we identified population structure on the third chromosome, which we attributed to a well-characterized inversion polymorphism. We assigned individual third chromosome haplotypes to inversion arrangements, demonstrating how tests for population structure can be used to identify polymorphic chromosomal rearrangements. Tajima's D was negative across most of the genome, consistent with a recent population expansion. However, the distribution of genetic variation differed across third chromosome inversion arrangements in ways that were consistent with their hypothesized evolutionary histories, and we identified inter-arrangement genetic differentiation that could be attributed to the inversions suppressing genetic exchange. The population genomic data we have collected are publicly available and will support future research on evolutionary genetics.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148648462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Mid-Atlantic Brook Trout (Salvelinus fontinalis) genome to advance conservation and comparative genomics.","authors":"Samuel W Rosenbaum, Merly Escalona, Samuel A May, Andrew R Whiteley","doi":"10.1093/g3journal/jkag209","DOIUrl":"10.1093/g3journal/jkag209","url":null,"abstract":"<p><p>Brook Trout (Salvelinus fontinalis) are experiencing genomic erosion and demographic declines across the southern portion of their native distribution. A regionally representative reference genome is necessary to support conservation genomic initiatives for this species. While Brook Trout exhibit substantial phylogenetic structure across their range, only a single reference genome from Northeastern Canada (ASM2944872v1) is currently used to guide range-wide analyses. Consequently, reference bias is expected to cause erroneous sequence alignment and spurious variant detection for Brook Trout from divergent lineages. To prevent reference bias and invalid inference when studying Mid-Atlantic Brook Trout, we assembled a de novo, chromosome-level genome using a wild individual from Virginia, USA and produced a gene annotation with publicly available RNA-seq data. The assembly combined three complementary sequencing types (PacBio HiFi, Oxford Nanopore Ultra-Long, and Dovetail Omni-C) and benefited from manual curation using the Pretext software suite. The 2.91 Gb genome, known as mSalvFont1.0, consists of 3,333 contigs (N50 = 3.3 Mb) and 1,299 scaffolds (N50 = 55 Mb), with 81% of the assembly contained within 42 chromosome-scale scaffolds. Indices of accuracy and completeness reveal a quality value of 59 (99.999% accuracy), k-mer completeness of 95%, and 99.3% complete BUSCOs from the Actinopterygii orthologous gene set. Additionally, we identified reference bias (26.94% heterozygosity inflation) when variant detection of a Mid-Atlantic-origin sample relied on alignment to ASM2944872v1, instead of mSalvFont1.0. We anticipate that mSalvFont1.0 will increase the accuracy and precision of regional conservation genomic initiatives and expedite the genesis of a Brook Trout pangenome.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13643803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148653331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}