G3: Genes|Genomes|Genetics最新文献

{"title":"Spontaneous hypopigmentation mutant in threespine stickleback fish exhibits changes in the gut microbiome consistent with inflammatory bowel diseases.","authors":"Emily A Beck, Caitlin A Smith, Mark C Currey, Clayton M Small, Brendan J M Bohannan, William A Cresko","doi":"10.1093/g3journal/jkag284","DOIUrl":"https://doi.org/10.1093/g3journal/jkag284","url":null,"abstract":"<p><p>Albinism is a large group of disorders characterized by a loss of pigment in ectoderm-derived tissues - most noticeably impacting the skin, hair, and eyes. Albinism is categorized as either syndromic or non-syndromic. Syndromic albinisms include a wide range of disorders with mutations impacting not just pigmentation but other cellular functions. These include, non-exclusively, melanogenesis disorders, endosome trafficking disorders like lysosomal storage disorders, and cell migration disorders. Mutations leading to syndromic albinisms can cause multi-organ system symptoms due to broad disruption lysosome related organelles (LROs) function. Various genetic mutations impact biogenesis, cell maturation, or trafficking at different stages which can lead to a range of severity. Syndromic albinisms also present with different combinations of symptoms depending on the impacted organelles; including oculocutaneous albinism (OCA) (melanosomes), blood diathesis (platelet dense granules), pulmonary fibrosis (lamellar bodies), or chronic inflammation (multiple cellular sources). Animal models for these multisymptomatic complex disorders are needed to understand the effects on systemic health. One such area of interest is in gut health of those with syndromic albinism. Shared inflammatory patterns of syndromic albinisms like Hermansky-Pudlak Syndromes (HPS) and Inflammatory Bowel Disease (IBD) are well studied, with animal models of HPS jointly used to study patterns of inflammation in IBD. However, the impact of this shared gastrointestinal inflammation on the gut microbiome remains unexplored. Using a spontaneously identified mutant family of threespine stickleback fish, we characterize phenotypes consistent with oculocutaneous albinism and vision impairment and demonstrate shared features of gut health to IBD extend from inflammation to the gut microbiome. We argue syndromic albinism models should be explored as models to study the gut microbiome in addition to inflammatory phenotypes in IBD, and importantly, be used to test microbial/dietary interventions for both IBD and syndromic albinisms.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192582","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 winter wheat GWAS identifies a large effect FHB resistance haplotype using diverse lines from U.S. breeding programs.","authors":"Lawrence Tidakbi, Hongliang Wang, Amy Bernardo, Paul St Amand, Allan Fritz, Guorong Zhang, Myron Bruce, Jessica L Rupp Noller, Gina Brown-Guedira, Guihua Bai, John Fellers, Mary J Guttieri, Katherine W Jordan","doi":"10.1093/g3journal/jkag291","DOIUrl":"https://doi.org/10.1093/g3journal/jkag291","url":null,"abstract":"<p><p>Fusarium head blight (FHB), primarily caused by Fusarium graminearum in North America, is a devastating disease in bread wheat (Triticum aestivum L.). The characteristic mycotoxin production and reduced grain fill cause several million metric tons of annual crop and economic losses. Exome capture-generated single nucleotide polymorphisms (SNPs) from 269 winter wheat breeding lines and cultivars representing most U.S. wheat-growing regions, were associated with FHB resistance using a genome-wide association study (GWAS). The panel was evaluated for FHB symptoms in the Rocky Ford FHB nursery (Manhattan, KS) across three field seasons. Significant variation was observed for FHB incidence (INC, %), area under the disease progress curve (AUDPC), Fusarium-damaged kernels (FDK, %), and deoxynivalenol (DON, ppm). Data analysis revealed significant FHB disease trait correlations (r = 0.32-0.70) across years and moderate broad-sense heritability (H2) estimates (0.65-0.74). We identified 22 significant loci representing priority breeding targets combating FHB damage. Many loci reside within proximity to previously identified native quantitative trait loci (QTL). A 1BL haplotype from the soft winter wheat cultivar 'Jamestown' reduced AUDPC and FDK by 25% and DON by 18%, demonstrating FHB resistance in an environment different from its native environment. We developed KASP assays to identify this resistance haplotype, and five other target SNPs for future incorporation in breeding pipelines increasing FHB resistance. Our findings highlight breeding progress demonstrated by the increased frequency of many resistant alleles in adapted varieties and breeding lines and emphasizes pyramiding native FHB resistance regions as the next step to prevent FHB losses.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149192510","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: sequencing of Helicoverpa-infecting Ophryocystis sp. confirms cryptic diversity and changes in gene content of Lepidoptera-infecting apicomplexan parasites.","authors":"Andrew J Mongue, Peter Kuperus, Astrid T Groot","doi":"10.1093/g3journal/jkag290","DOIUrl":"https://doi.org/10.1093/g3journal/jkag290","url":null,"abstract":"<p><p>Apicomplexan parasites of insects represent a largely unexplored branch of the tree of life. Their small size and lack of informative phenotypic traits can obscure their diversity and many lineage-specific adaptations to different host species. To better understand how these parasites have evolved, we have sequenced and annotated the genome of a neogregarine parasite of moths in the family Noctuidae, including Helicoverpa armigera. This parasite, which we term Helicoverpa-infecting Ophryocystis, has a tiny 8 Megabase genome with only 2,500 predicted protein-coding genes. Using phylogenomic methods, we placed it as the closest currently sequenced relative to Ophryocystis elektroscirrha and its sister lineage, both of which infect milkweed butterflies (Lepidoptera: Nymphalidae). We also explored the conservation of gene families, with a specific focus on the evolution of the ATPase gene family, as this is thought to be reduced in other Ophryocystis lineages. We found that our newly sequenced lineage also lacks any sodium pump ATPases, while all other types are conserved. Our results demonstrate the utility of applying modern genomic approaches to gaining insights into the evolution of insect-infecting Apicomplexa, but also shows that much remains to be discovered.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180576","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":"IDEAL-GENOM: integrated downstream analytical toolkit for genomic analysis.","authors":"Luis Giraldo González Ricardo, Amabel M M Tenghe, Ashwin Ashok Kumar-Sreelatha, Manu Sharma","doi":"10.1093/g3journal/jkag283","DOIUrl":"https://doi.org/10.1093/g3journal/jkag283","url":null,"abstract":"<p><p>There has been an exponential increase in the development of technologies that have offered unprecedented opportunities to unravel the genetic underpinnings of complex traits. However, despite the progress and availability of tools, there are still several challenges to overcome, such as the development of a unified framework that facilitates downstream analysis. To address this challenge, we present IDEAL-GENOM (Integrated Downstream Evaluation And anaLysis toolkit for GENOMic data), a Python-based wrapper designed to streamline the analytical workflow commonly implemented in binary (case-control) genome-wide association studies (GWAS). IDEAL-GENOM integrates widely used tools such as PLINK, GCTA, and bcftools along with custom-developed functionalities, enabling reproducible results through parameter sharing. IDEAL-GENOM provides a simplified framework for quality control (QC), GWAS, and downstream analysis that will enable beginners and advanced users to leverage the built-in functionalities to perform GWAS analysis for complex traits with binary outcomes. IDEAL-GENOM is a customizable tool that enables users to efficiently analyze genotyping data with reproducible QC, post-imputation, and GWAS pipelines.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149180597","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":"Genetic loci resistant to soybean southern stem canker in Tracy-M and its progeny.","authors":"M Habib Widyawan, James W Buck, Zenglu Li","doi":"10.1093/g3journal/jkag278","DOIUrl":"https://doi.org/10.1093/g3journal/jkag278","url":null,"abstract":"<p><p>Southern stem canker (SSC), caused by Diaporthe aspalathi, is a major soybean disease causing yield losses of up to 80%. Genetic resistance is the most effective and sustainable strategy for managing SSC. \"Tracy-M\" is a cultivar with broad resistance to D. aspalathi isolates; however genomic location of the resistance is unknown. To determine the genetic basis of SSC resistance in Tracy-M and its derived progeny, two Tracy-M-derived lines, D85-10404 and D85-10412, were each crossed with a common susceptible parent, G81-2057, to develop recombinant inbred line (RIL) populations. Quantitative Trait Locus (QTL) sequencing (QTL-seq) and composite interval mapping (CIM) identified a common major QTL on chromosome (Chr) 2 in both lines corresponding to Rdm1 locus defined from a previous genetic study. Additionally, second QTL located on Chr 17 (Rdm2 locus) was only detected in the D85-10412-derived RIL population. To validate Tracy-M-derived resistance, an F2:3 population from G00-3213 × Tracy-M was developed. Bulked segregant analysis (BSA) and CIM identified a major QTL on Chr 14, overlapping the previously reported Rdm3 locus in \"Crockett\" and PI 398469, while Rdm1 was not detected, suggesting genetic background effects. Kompetitive allele-specific PCR (KASP) markers were developed to facilitate selection of Rdm1, Rdm2, and Rdm3 resistance alleles in soybean breeding programs.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149167969","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 genome assembly of Coprinellus radians.","authors":"Manman Yu, Yuxue Cheng, Yuxin Shan, Hong To Quyen Duong, Somnuk Bunsupa, Xiaohui Tong, Rongchun Han","doi":"10.1093/g3journal/jkag267","DOIUrl":"https://doi.org/10.1093/g3journal/jkag267","url":null,"abstract":"<p><p>Coprinellus radians has been identified as an important germination-associated fungus of Cremastra appendiculata. However, no reference genome was previously available for this species. In this study, we generated a complete telomere-to-telomere (T2T) genome assembly for C. radians by integrating PacBio HiFi, Oxford Nanopore, BGI short-read, and Hi-C sequencing data. Hi-C interaction mapping anchored 99.36% of the assembled sequences onto 13 pseudochromosomes. Following contaminant removal, gap closure using TGS-GapCloser, and telomere extension, the final assembly consists of 13 gap-free, single-contig chromosomes with telomeric repeats (CCCTAA/TTAGGG) at both ends, yielding a total of 26 telomeres. The resulting high-quality genome is 41.09 Mb (41,092,644 bp) in size, with a contig N50 of 3.36 Mb and a BUSCO completeness score of 96.4%. This gap-free, T2T genome provides a valuable resource for investigating the molecular mechanisms of orchid-fungus symbiosis and the ecological adaptation of wood-decaying fungi.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135816","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":"Genetic analysis of bone morphometry and ivory vertebrae in threespine stickleback.","authors":"Veronica C Behrens, David Lee, Julia I Wucherpfennig, David M Kingsley","doi":"10.1093/g3journal/jkag164","DOIUrl":"10.1093/g3journal/jkag164","url":null,"abstract":"<p><p>Previous genetic studies of skeletal variation in threespine stickleback fish (Gasterosteus aculeatus) have focused primarily on striking morphological differences. Here, we examine the largely unexplored genetic architecture of internal bone microstructural variation between marine and freshwater stickleback. Micro-computed tomography X-ray analysis revealed differences in the porosity, bone thickness, and bone volume fraction within armor plates and vertebrae from a marine and freshwater stickleback. Quantitative trait locus mapping in F2 progeny from a marine × freshwater stickleback cross identified a significant locus on chromosome 4 influencing multiple aspects of armor plate internal microstructure. This locus overlaps the well-characterized Eda region previously known to control armor plate number and size. Co-mapping of bone microstructure could be due to pleiotropic effects of Eda on multiple aspects of plate development or to changes in closely linked genes including Itm2a, which also plays a role in bone formation. Most bone microstructure traits in vertebrae showed weak or no genetic signal, consistent with a polygenic architecture. However, we identified a highly significant locus on chromosome 17 that is strongly associated with abnormally thickened \"ivory vertebrae\" that occurred in 8.4% of F2 offspring. This phenotype resembles Paget's disease in humans, and the major locus region contains Tnfrsf1b, the stickleback ortholog of a human Paget's disease susceptibility gene TNFRSF11A. Together, our findings identify genetic loci underlying natural variation in bone microstructure in wild fish and reveal a candidate gene associated with a disease-like skeletal phenotype, highlighting stickleback as a model for studying both evolutionary and pathological bone biology.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135833","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":"Large-scale gain-of-function analysis reveals distributed genetic contributions to activity persistence under oxidative stress in Drosophila.","authors":"Toru Togawa, Manabu Tsuda, Takashi Matsuo, Toshiro Aigaki","doi":"10.1093/g3journal/jkag277","DOIUrl":"https://doi.org/10.1093/g3journal/jkag277","url":null,"abstract":"<p><p>Organismal responses to stress are often assessed by survival, yet the genetic basis of sustained functional performance under stress remains poorly understood. Here, we performed a large-scale gain-of-function analysis in Drosophila melanogaster using 2,838 Gene Search (GS) insertion lines that enable GAL4-dependent activation of nearby loci. Adult flies were exposed to hydrogen peroxide, and spontaneous locomotor activity was monitored at high temporal resolution to quantify activity persistence, defined as the duration of activity until sustained cessation under oxidative challenge. A primary screen identified candidate lines, which were then subjected to quantitative reassessment. Most perturbations did not improve activity persistence, whereas only a small subset reproducibly enhanced the phenotype. We identified 26 loci that reproducibly extended activity persistence, 23 of which required GAL4, consistent with activation of nearby loci by GS insertions. The associated loci encompass diverse functional categories, including transcriptional and chromatin regulators, signaling components, metabolic and mitochondrial factors, and structural proteins. These findings indicate that stress-dependent activity persistence is governed by distributed genetic contributions spanning diverse biological functions rather than a single dominant pathway.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149127099","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":"Correction to: Nematode-resistance loci in upland cotton genomes are associated with structural differences.","authors":"","doi":"10.1093/g3journal/jkag184","DOIUrl":"10.1093/g3journal/jkag184","url":null,"abstract":"","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/PMC13643809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148410908","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 signatures of cold adaptation in a Himalayan drosophilid.","authors":"Avirup Chakraborty, Subhash Rajpurohit","doi":"10.1093/g3journal/jkag190","DOIUrl":"10.1093/g3journal/jkag190","url":null,"abstract":"<p><p>Drosophila nepalensis is a cold-adapted drosophilid endemic to the Himalayan region. Its ability to survive in harsh, cold conditions makes it a valuable Drosophila model for investigating how adaptation to thermal extremes may influence species persistence under future climate change. Here, we report the first de novo genome assembly of D. nepalensis, based on a hybrid sequencing strategy that combines Illumina short reads and Oxford Nanopore long reads. Illumina sequencing generated 49.88 million 150 bp paired-end reads (∼14.96 Gbp), while Nanopore sequencing produced 1.35 million long reads totaling ∼0.76 Gbp. The assembled genome spanned ∼178 Mb with an N50 of 83.6 kb and 98% BUSCO completeness, comparable to other well-annotated Drosophila genomes. Annotation identified 10,560 protein-coding genes, including transcription factor-rich and stress-related domains such as zinc fingers, WD40 repeats, and ankyrin motifs. Comparative orthology analysis across 6 Drosophila species identified 14,168 orthologous clusters, of which 9,173 were shared among all 6 species, indicating a conserved core genomic set across the sampled taxa. D. nepalensis showed 83 unique orthogroups and 50 singletons, suggesting some lineage-specific gene expansions associated with cold adaptation and endemicity, including families encoding caspase-family apoptotic regulators, chromatin remodeling proteins (HMGB/protamine-like), and SNARE-domain vesicle trafficking factors. Gene family evolution analysis revealed the highest expansions in the cold-tolerant Himalayan drosophilid, D. nepalensis, including significant expansions in serine protease, chaperone, and neurotransmitter transporter families, alongside dramatic contractions of core histone gene families, suggesting lineage-specific chromatin remodeling and ecological specialization.</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/PMC13643813/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886980","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}