G3: Genes|Genomes|Genetics最新文献

{"title":"Wild Strains Reveal Natural Variation in C. elegans Avoidance Behaviors.","authors":"Emily A Polk, Alber Aqil, J B Collins, Robyn E Tanny, Erik C Andersen, Omer Gokcumen, Denise M Ferkey","doi":"10.1093/g3journal/jkaf243","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf243","url":null,"abstract":"<p><p>Chemical stimuli, including odorants and tastants, provide information about food availability and allow animals to avoid harmful environments. Over six decades of research using primarily one laboratory-adapted strain of the nematode Caenorhabditis elegans has yielded a wealth of information about how this animal senses and responds to chemical cues to survive. However, it was not known whether the chemosensory behavioral profile of this strain (named N2) is representative of the species. Using a collection of hundreds of wild C. elegans strains collected from around the globe, we assessed their abilities to respond to three aversive stimuli (the bitter tastant quinine, the heavy metal copper, and the detergent SDS) in a laboratory setting and found ∼10-20 fold differences in response sensitivities among the strains. Further, response sensitivities to one stimulus were largely uncoupled from responses to the other stimuli and uncorrelated with the geographical locations from which the wild strains were collected. Using genome-wide association studies, we identified unique regions significantly correlated with different responses to each stimulus. Near-isogenic lines were created to confirm the effects of two genomic regions on differential avoidance behavior to the bitter tastant quinine. Combined, we report remarkable natural variation in chemosensory behavioral responses among wild C. elegans strains and describe two new quantitative trait loci associated with decreased response sensitivity to quinine.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274246","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":"Identification of Susceptibility Loci Using a Novel Murine Model for Triple Negative Breast Cancer.","authors":"Minjeong Kim, Logan G McGrath, Zeid T Mustafa, Samson Eugin Simon, Naveed Pervaiz, Emily W Grey, Sydney C Joseph, Emily Korba, Sandesh J Marathe, Margaret S Bohm, Arvind V Ramesh, Sidharth S Mahajan, Casey J Bohl, Pjotr Prins, Robert W Read, Jeremiah R Holt, D Neil Hayes, Lu Lu, Robert W Williams, Laura M Sipe, David G Ashbrook, Liza Makowski","doi":"10.1093/g3journal/jkaf238","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf238","url":null,"abstract":"<p><p>Triple negative breast cancer (TNBC) is the deadliest subtype of breast cancer (BC) with few targeted therapies. To identify novel genetic modifiers of TNBC, we created a murine model incorporating high levels of genetic and phenotypic diversity. C3(1)-T-antigen (\"C3Tag\") mice, which develop spontaneous basal-like TNBC tumors, were systematically crossed with a large set of sequenced BXD recombinant inbred strains to produce isogenic hybrids segregating for C3Tag. The severity of TNBC traits including tumor latency, multiplicity, and survival were highly variable and heritable. We mapped modifiers of TNBC and identified loci on chromosomes 16 and 10 associated with tumor multiplicity and latency, respectively. Candidate genes were prioritized including: a lysosomal enzyme involved in cell proliferation, Gns; tumor suppressor Rassf3; and Rab-modifying Tbc1d30. In tumors from BC patients, higher GNS, RASSF3, and TBC1D30 expression associated with poor overall survival. In sum, we developed a clinically relevant, BXD-BC model which provides robust genetic heterogeneity enabling the identification of conserved modifiers and mediators of BC.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274217","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":"Genome report: chromosome-scale genome assembly of the Olive fly Bactrocera oleae (Diptera: Tephritidae).","authors":"Thorsten E Hansen, Renee L Corpuz, Tyler J Simmonds, Charlotte Aldebron, Charles J Mason, Scott M Geib, Sheina B Sim","doi":"10.1093/g3journal/jkaf235","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf235","url":null,"abstract":"<p><p>The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is a specialist of Olea fruits and is a major pest of commercial olives due to their adverse impacts to fruit quality. In support of genomic and physiological research of the olive fly, we sequenced, assembled, and annotated two independent genomes: one from a wild-collected male and one from a wild-collected female. The resulting genomes are highly contiguous, collinear, and complete, attesting to the accuracy and quality of both assemblies. In addition to the autosomes captured as single contigs, the X and Y chromosomes were also identified as evidenced by the X chromosome showing diploid coverage in the female assembly compared to haploid coverage in the male assembly and the Y chromosome being entirely absent from the female assembly. These assemblies represent the first full chromosome-level assembly for olive fly. In addition, a complete genome assembly of a known obligate symbiont, Candidatus Erwinia dacicola, was fully sequenced. The Ca. E. dacicola genome we report here is the most contiguous to date, represented by a gapless chromosome and two separate gapless plasmids. These genome assemblies, along with bacterial symbiont assembly, provide foundational resources for future genetic and genomic research in support of its management as an agricultural pest.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145257628","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":"Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.","authors":"Lydia J M Fong, Bernadette D Johnson, Iulia Darolti, Benjamin A Sandkam, Judith E Mank","doi":"10.1093/g3journal/jkaf188","DOIUrl":"10.1093/g3journal/jkaf188","url":null,"abstract":"<p><p>The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. The close relatives Poecilia reticulata, Poecilia picta, and Poecilia parae all share the same sex chromosome system, but with substantial diversity in the degree of Y degeneration and the extent of X chromosome dosage compensation. In order to identify if P. bifurca shares the same sex chromosome system, we built a female (XX) draft genome with 55X coverage of PacBio HiFi data, resulting in a 785 Mb assembly with 94.4% BUSCO completeness. We used this genome and found that P. bifurca shares the same sex chromosomes as related species and shows substantial Y chromosome degeneration. We combined this with RNA-Seq data and found similar expression of X-linked genes between sexes, revealing that P. bifurca also exhibits complete X chromosome dosage compensation. We further identify 11 putative autosome-to-Y gene duplications, 5 of which show gene expression in guppy male germ cells.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506654/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144882552","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":"Accounting for gene flow from unsampled ghost populations while estimating evolutionary history.","authors":"Arun Sethuraman, Melissa Lynch, Margaret Wanjiku, Michael Kuzminskiy","doi":"10.1093/g3journal/jkaf180","DOIUrl":"10.1093/g3journal/jkaf180","url":null,"abstract":"<p><p>Gene flow from unsampled or extinct ghost populations leave signatures on the genomes of individuals from extant, sampled populations, often introducing biases, data misinterpretation, and ambiguous results when estimating evolutionary history from population genomic data. Here we establish theoretical expectations for these biases, and then utilize extensive simulations under a variety of ghost topologies to systematically assess biases while accounting, or not accounting for gene flow from ghost populations in (i) population genetics summary statistics such as π, FST, and Tajima's D and (ii) demographic history (mutation-scaled effective population sizes, divergence times, and migration rates) under the Isolation with Migration (IM) model. Estimates of evolutionary history across all scenarios of deep divergence of an outgroup ghost indicate consistent (i) under-estimation of divergence times between sampled populations, (ii) over-estimation of effective population sizes of sampled populations, and (iii) under-estimation of migration rates between sampled populations, with increased gene flow from the unsampled ghost population. Without accounting for an unsampled ghost, summary statistics like FST are under-estimated, and π is over-estimated with increased gene flow from the ghost. These biases in summary statistics and population structure are however not captured under models of recent IM that approximate scales of the evolution of anatomically modern humans and Neanderthals and solely recapitulated using model-based estimation of evolutionary history. We also utilize a 355 locus dataset from African Hunter-Gatherer populations and discuss similar biases in estimating evolutionary history while not accounting for unsampled ghost.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834728","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":"Unilateral loss of recql4 function in Xenopus laevis tadpoles leads to ipsilateral ablation of the forelimb, hypoplastic Meckel's cartilage, and vascular defects.","authors":"Caroline W Beck, Matthew Reily-Bell, Louise S Bicknell","doi":"10.1093/g3journal/jkaf179","DOIUrl":"10.1093/g3journal/jkaf179","url":null,"abstract":"<p><p>RECQL4 encodes a RecQ helicase, one of a family of DNA unwinding enzymes with roles in DNA replication, double-strand break repair, and genomic stability. Pathogenic variants in RECQL4 are clinically associated with 3 rare autosomal recessive conditions: Rothmund-Thomson syndrome type II, Baller-Gerold syndrome, and RAPADILINO syndrome. These 3 syndromes show overlapping growth retardation, low bone density, and skeletal defects affecting the arms and hands. Here, we take advantage of the ability to generate one-sided CRISPR knockdowns of recql4 in Xenopus laevis tadpoles. Tadpoles develop normally until feeding starts, after which growth slows on the edited side, leading to a curved posture, smaller eyes (microphthalmia), and reduced head size (microcephaly). Forelimb buds fail to develop, leading to complete absence of the forelimb on the edited side. Additionally, Meckel's cartilage (lower jaw) ossification is absent or reduced and the hyoid cartilage is smaller, but this is not due to deficiencies in cranial neural crest migration on the edited side. Knockdown of recql4 also results in hypoplastic vasculature, with reduced branching from the aorta on the edited side. Taken together, our results clearly show the utility of unilateral CRISPR editing in Xenopus for understanding the specific phenotypic developmental effects of mutations affecting cell proliferation.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144862237","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":"Annotated genome of the Atlantic dog whelk, Nucella lapillus.","authors":"Meghan R Ford, Steven V Vollmer, Geoffrey C Trussell","doi":"10.1093/g3journal/jkaf182","DOIUrl":"10.1093/g3journal/jkaf182","url":null,"abstract":"<p><p>Nucella lapillus is an important player in rocky shore food chains and has been a focal organism of ecological and evolutionary studies for decades. Despite poor dispersal, they have a broad geographic range, which makes them an ideal species to examine isolation by distance and selection across environmental gradients. Here we present the fully annotated genome of N. lapillus generated with Oxford Nanopore Techonology sequencing at ∼37× coverage. The genome assembly is 2.32 Gbp and consists of 2,525 contigs, with an N50 length of 2 Mbp. Repeat annotation identified 2,491 families that cover 67.56% of the genome, which is similar to other gastropods. Despite its large size and high proportion of repeats, the genome is of high quality. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis revealed a score of 96.8%. Functional annotation of the genome produced 45,848 protein-coding genes with a 96.6% BUSCO score. Genomic resources for mollusks lag behind that of other phyla, perhaps because many of their innate characteristics complicate DNA extraction, sequencing, and assembly. This new N. lapillus genome will increase our genomic understanding of the second largest phylum (and the most diverse class within said phylum) and serve as a key resource to advance studies on the organismal biology and population genetics of this iconic species as well as the connection between genomic variation and community-level processes.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834729","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":"Direct and transgenerational effects of tetracyclines on the microbiome, transcriptome, and male mating behavior of the sheep blowfly Lucilia cuprina.","authors":"Alexis L Kriete, Maxwell J Scott","doi":"10.1093/g3journal/jkaf160","DOIUrl":"10.1093/g3journal/jkaf160","url":null,"abstract":"<p><p>Tetracyclines are broad-spectrum antibiotics widely used in agriculture, medicine, and research. However, they are associated with harmful side effects. In arthropods, parental exposure to tetracyclines has been linked to reduced health and fitness in untreated offspring. These transgenerational effects of tetracyclines could jeopardize the success of pest control programs that use tetracyclines to control gene expression. In this study, we investigated the transgenerational effects of 2 tetracyclines, doxycycline (DOX) and anhydrotetracycline (ATC), in the blowfly Lucilia cuprina, a significant pest of sheep. To simulate the rearing conditions of a transgenic male-only release program, blowflies were reared on standard diet alone, or standard diet plus DOX or ATC, for 3 generations, and then reared for an additional fourth generation on standard diet alone. We used behavioral assays, 16S amplicon sequencing, and mRNA sequencing to determine how DOX and ATC influenced male sexual competitiveness, microbiome composition, and gene expression in the third and fourth generations. We found that 3 generations of DOX treatment led to lower sexual competitiveness in both third- and fourth-generation males. In addition, DOX and ATC shifted the composition of the blowfly microbiome and altered the expression of numerous mitochondria- and immunity-related genes in both generations. Our study supports an emerging body of evidence that tetracyclines exert not only direct but also transgenerational effects, and sheds light on the transcriptional and microbial responses to antibiotic exposure and removal. Our findings emphasize the need for pest control programs that use tetracyclines to evaluate the long-term effects of these antibiotics.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642199","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":"The genome of Chenopodium ficifolium: developing genetic resources and a diploid model system for allotetraploid quinoa.","authors":"Clayton D Ludwig, Peter J Maughan, Eric N Jellen, Thomas M Davis","doi":"10.1093/g3journal/jkaf162","DOIUrl":"10.1093/g3journal/jkaf162","url":null,"abstract":"<p><p>High-quality nuclear, chloroplast, and preliminary mitochondrial genomes have been assembled and annotated for the B genome diploid (BB: 2n = 2x = 18) figleaf goosefoot (Chenopodium ficifolium). The primary objective was to advance a simplified model system for genetic characterization and improvement of allotetraploid (AABB: 2n = 4x = 36) quinoa (Chenopodium quinoa), a nutritionally valuable, halophytic orphan crop. In addition to its diploidy and favorably small genome size, the C. ficifolium model provides a shorter generational period and smaller overall plant size as compared to C. quinoa, while displaying relevant agronomic trait variations amenable to gene-trait association studies. The C. ficifolium \"Portsmouth\" nuclear genome was sequenced using PacBio HiFi long-read technology and assembled using Hifiasm. After manual adjustments, the final ChenoFicP_1.0 assembly consisted of 9 pseudochromosomes spanning 730 Mbp, while 22,617 genes were identified and annotated. BUSCO analyses indicated a nuclear genome completeness of 97.5% and a proteome and transcriptome completeness of 98.4%. The chloroplast genome assembly detected 2 equally represented structural haplotypes differing in the orientation of the short single copy region relative to the long single copy region. Phylogenetic and parentage analyses pointed to an unspecified AA diploid species and away from C. ficifolium as the likely maternal chloroplast and mitochondrial genome donor(s) during the initial tetraploidization event in the C. quinoa lineage. Using the new ChenoFicP_1.0 reference genome, a genome-wide association study was performed on a previously studied C. ficifolium F2 population to further define region(s) implicated in the control of 3 key agronomic traits: days to flowering, plant height, and branch number. This analysis localized control of all 3 traits to a 7-Mb interval on pseudochromosome Cf4. This region contains ∼770 genes, including the FTL1 locus, thus confirming and extending our prior, single-marker analysis showing association of these 3 traits with an FTL1 amplicon length polymorphism. The use of these data to further develop C. ficifolium as a model species for genetics and breeding of quinoa serves to expand knowledge and germplasm resources for quinoa improvement.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12506657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144663891","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":"Congenital heart disease missense mutations in the TBX5 DNA-binding domain alter thermal stability and DNA-binding affinity.","authors":"Alejandro Rivera-Madera, Edwin G Peña-Martínez, Jean L Messon-Bird, Diego A Pomales-Matos, Oswaldo L Echevarría-Bonilla, Leandro Sanabria-Alberto, Esther A Peterson-Peguero, José A Rodríguez-Martínez","doi":"10.1093/g3journal/jkaf174","DOIUrl":"10.1093/g3journal/jkaf174","url":null,"abstract":"<p><p>Missense mutations can alter the biochemical properties of proteins, including stability, structure, and function, potentially contributing to the development of multiple human diseases. Mutations in TBX5, a transcription factor necessary for heart development, are among the causes of congenital heart diseases. However, further research on biophysical and biochemical mechanisms is needed to understand how missense mutations in transcription factors alter their function in regulating gene expression. In this work, we applied in vitro and in silico approaches to understand how 5 missense mutations in the TBX5 T-box DNA-binding domain (I54T, M74V, I101F, R113K, and R237W) impact protein structure, thermal stability, and DNA-binding affinity to known TBX5 cognate binding sites. Differential scanning fluorimetry showed that mutants I54T and M74V had decreased thermal stability, mutants I101F and R113K had increased stability, and R237W had no significant effect on stability. Additionally, DNA-binding affinity decreased for all 5 missense mutants when evaluated in vitro for known TBX5 genomic binding sites within regulatory elements of Nppa and Camta1 genes. Structural modeling of the TBX5 predicted altered protein conformations and stability due to the loss or gain of amino acid residue interactions. Together, our findings provide biophysical and biochemical mechanisms that can be further explored to establish causality between TBX5 missense mutations and the development of congenital heart diseases.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144764807","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}