G3: Genes|Genomes|Genetics最新文献

{"title":"Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.","authors":"Valérie de Crécy-Lagard, Raquel Dias, Nick Sexson, Iddo Friedberg, Yifeng Yuan, Manal A Swairjo","doi":"10.1093/g3journal/jkaf169","DOIUrl":"10.1093/g3journal/jkaf169","url":null,"abstract":"<p><p>Thirty to seventy percent of proteins in any given genome have no assigned function and have been labeled as the protein \"unknome.\" This large knowledge shortfall is one of the final frontiers of biology. Machine learning (ML) approaches are enticing, with early successes demonstrating the ability to propagate functional knowledge from experimentally characterized proteins. An open question is the ability of ML approaches to predict enzymatic functions unseen in the training sets. By integrating literature and a combination of bioinformatic approaches, we evaluated individually Enzyme Commission number predictions for over 450 Escherichia coli unknowns made using state-of-the-art ML approaches. We found that current ML methods not only mostly fail to make novel predictions but also make basic logic errors in their predictions that human annotators avoid by leveraging the available knowledge base. This underscores the need to include assessments of prediction uncertainty in model output and to test for \"hallucinations\" (logic failures) as a part of model evaluation. Explainable artificial intelligence analysis can be used to identify indicators of prediction errors, potentially identifying the most relevant data to include in the next generation of computational models.</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/PMC12506659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144698101","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 factors limiting the diversity of Saccharomycotina plant pathogens.","authors":"Sun Lee, Caroline West, Dana A Opulente, Marie-Claire Harrison, John F Wolters, Xing-Xing Shen, Xiaofan Zhou, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas, Abigail Leavitt LaBella","doi":"10.1093/g3journal/jkaf184","DOIUrl":"10.1093/g3journal/jkaf184","url":null,"abstract":"<p><p>The Saccharomycotina fungi have evolved to inhabit a vast diversity of habitats over their 400-million-year evolution. There are, however, only a few known fungal pathogens of plants in this subphylum, primarily belonging to the genera Eremothecium and Geotrichum. We compared the genomes of 12 plant-pathogenic Saccharomycotina strains with 360 plant-associated strains to identify features unique to the phytopathogens. Characterization of the oxylipin synthesis genes, a compound believed to be involved in Eremothecium pathogenicity, did not reveal any differences in gene presence within or between the plant-pathogenic and plant-associated strains. A reverse-ecological approach, however, revealed that plant pathogens lack several metabolic enzymes known to assist other phytopathogens in overcoming plant defenses. This includes L-rhamnose metabolism, formamidase, and nitrilase genes. This result suggests that the Saccharomycotina plant pathogens are limited to infecting ripening fruits as they are without the necessary enzymes to degrade common phytohormones and secondary metabolites produced by plants.</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/PMC12506670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834756","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":"MLDAAPP: machine learning data acquisition for assessing population phenotypes.","authors":"Amir R Gabidulin, Seth M Rudman","doi":"10.1093/g3journal/jkaf173","DOIUrl":"10.1093/g3journal/jkaf173","url":null,"abstract":"<p><p>Collecting phenotypic data from many individuals is critical to answering fundamental biological questions, particularly in genetics. Yet, whole organismal phenotypic data are still often collected manually; limiting the scale of data generation, precluding reproducible workflows, and creating potential bias. Computer vision can ameliorate these issues, but currently available packages only operate with specific inputs and have limited scalability. We present Machine Learning Data Acquisition for Assessing Population Phenotypes (MLDAAPP), a package of tools built on YOLOv8 for collecting phenotypic data from groups of individuals that is flexible for generating counts (e.g. Drosophila fecundity, census), movement (e.g. activity, aversive behavior), and many other potential phenotypes. MLDAAPP is both accurate and uniquely effective for obtaining phenotypic data in challenging conditions-particularly images and videos of varying quality derived from both lab and field environments. Employing MLDAAPP solves key issues of reproducibility and increases the scale and scope of data generation.</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/PMC12506647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144759660","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":"Somatic gonad morphogenesis in C. elegans requires the heterochronic pathway acting through HBL-1.","authors":"Madeleine Minutillo, Kevin Kemper, Maria Ivanova, Erika Pianin, Eric G Moss","doi":"10.1093/g3journal/jkaf170","DOIUrl":"10.1093/g3journal/jkaf170","url":null,"abstract":"<p><p>Heterochronic genes are known for acting in succession to control the timing of stage-specific events of the developing Caenorhabditis elegans larva. While most heterochronic mutants have normal gonad development, in a few cases, defective timing regulators lead to variations in gonad development, although with little to no effect on fertility. We found that a double mutant of 2 heterochronic genes, a lin-28 null allele and hbl-1 hypomorphic allele, results in a catastrophic failure of gonad morphogenesis resulting in sterility. This defect includes a high-penetrance disruption of normal gonad arm migration as well as frequent absence of 1 or both spermathecae. We demonstrate that the abnormal gonad morphology and novel sterility phenotype is ultimately due to loss of hbl-1 activity in larval development. To clarify the mechanism of how lin-28 positively influences hbl-1 activity, we demonstrate a direct interaction between the RNA-binding protein LIN-28 and the 5'UTR of lin-46, and in turn, a direct interaction between LIN-46 and 2 zinc fingers of HBL-1. Nevertheless, our genetic analysis indicates that lin-46 accounts for only part of lin-28's regulation of hbl-1 and that some portion of lin-28's effect is independent of lin-46.</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/PMC12506653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729301","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":"Identification of the putative gene encoding the RNA subunit of telomerase in Malassezia clade species through comparative genomic analysis.","authors":"Juan Antonio Sanpedro-Luna, Patricia Sanchez-Alonso","doi":"10.1093/g3journal/jkaf185","DOIUrl":"10.1093/g3journal/jkaf185","url":null,"abstract":"<p><p>Maintaining telomere length and genomic stability in eukaryotic cells is dependent on telomerase, a ribonucleoprotein with reverse transcriptase activity that counteracts the end replication problem. Its core components include telomerase reverse transcriptase (TERT) and telomerase RNA (TER). This study focused on the identification of the putative MgTER gene, which encodes the telomerase RNA subunit, in Malassezia globosa through comparative genomics. Unlike the corresponding genes in other yeasts and filamentous fungi, this gene is compact and uniform in length, resembling similar genes in vertebrates, while retaining characteristic elements that are crucial for TER and snRNA biogenesis and activity. These elements include the template domain, pseudoknot domain, CR4/5 domain, and a putative Sm-binding site. Furthermore, transcriptomic analysis confirmed the transcriptional activity of the putative MgTER gene, reinforcing its potential functional significance within this organism. These results establish a robust basis for future experimental investigations to verify the functionality and regulatory mechanisms of this gene, particularly its role in telomere maintenance and broader cellular 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/PMC12506658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144872402","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":"New reference genome assembly for the declining American Bumble Bee, Bombus pensylvanicus.","authors":"Jeffrey D Lozier, Rena M Schweizer, Sheina B Sim, Jonathan Berenguer Uhuad Koch, Michael G Branstetter, Ligia R Benavides, Scott M Geib, Jay D Evans","doi":"10.1093/g3journal/jkaf181","DOIUrl":"10.1093/g3journal/jkaf181","url":null,"abstract":"<p><p>We present the first chromosome-level genome assembly for Bombus pensylvanicus, a historically widespread native pollinator species that was distributed across eastern North America but has subsequently undergone declines in range area and local relative abundance. This species has been of significant interest as a model for understanding both patterns and possible causes of bumble bee decline in the region, including the role of genetic variation. Here we present a chromosome-level reference genome assembled using Pacific Biosciences singe-molecule HiFi sequences and Hi-C data and annotated using evidence derived from RNA sequencing of multiple tissue types. The B. pensylvanicus genome has a total length of ∼352.6 Mb and was assembled into a total of 224 scaffolds, with 19 primary pseudomolecules representing putative chromosomes and an N50 = 14.872 Mb. Annotation with the Eukaryotic Genome Annotation Pipeline-External (EGAPx) identified 11,411 genes (10,263 protein coding), and BUSCO analysis of 5,991 Hymenoptera-specific BUSCO groups indicated a completeness for the proteins of 99.0% (98.6% single-copy, 0.5% duplicated) and for the genome of 98.5% (98.2% single-copy, 0.3% duplicated). We present synteny analyses with other recently assembled Bombus genomes representing different subgenera and examine the distribution of repetitive regions of the genome relative to the distribution of genes and noncoding RNAs.</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/PMC12506661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834758","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":"Chromosome level assembly and annotation of Cuscuta campestris Yunck. (\"field dodder\"), a model parasitic plant.","authors":"Juan D Cerda-Herrera, Huiting Zhang, Eric K Wafula, Supral Adhikari, So-Yon Park, Sarah B Carey, Alex Harkess, Paula E Ralph, James H Westwood, Michael J Axtell, Claude W dePamphilis","doi":"10.1093/g3journal/jkaf193","DOIUrl":"10.1093/g3journal/jkaf193","url":null,"abstract":"<p><p>We present the first chromosome-level genome assembly and annotation for the genus Cuscuta, a twining and leafless parasitic plant of the morning glory family (Convolvulaceae). C. campestris, the study species, is a widely studied model parasite, due in part to its worldwide occurrence as a weed of agricultural and natural plant communities. The species has served as a model parasite for studies of parasite biology, haustorium development, growth responses to chemical and light stimuli, gene content and expression, horizontal gene transfer, and interspecies RNA movement and has a recently developed transformation system. The 505 Mb (1C) genome is assembled into 31 chromosomes and supports annotation of 47,199 protein-coding genes, 214 small RNA loci (including 146 haustoria-specific miRNAs), and 3,238 interspecies mobile mRNA loci. C. campestris is a recent tetraploid with a high retention of duplicated genes and chromosomes, with less than 8% nucleotide divergence between homoeologous chromosomes. We also show that transformation of C. campestris with the RUBY marker system allows visualization of transformed Cuscuta-derived fluorescent mobile molecules that have entered the host stem. This genome, with an associated genome browser and BLAST server, will be of value for scientists performing fundamental research in a wide range of molecular, developmental, population, and evolutionary biology, as well as serve as a research tool for studying interspecies mobile molecules, generating genetic markers for species and genotype identification, and developing highly specific herbicides.</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/PMC12506650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144882551","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":"Bayesian divergence-based approach for genomic multitrait ordinal selection.","authors":"Bartolo de J Villar-Hernández, Pawan Singh, Nerida Lozano-Ramírez, Paolo Vitale, Guillermo Gerard, Flavio Breseghello, Susanne Dreisigacker, José Crossa","doi":"10.1093/g3journal/jkaf183","DOIUrl":"10.1093/g3journal/jkaf183","url":null,"abstract":"<p><p>Effective genomic selection for ordinal traits, such as disease resistance scores, is a persistent challenge in plant breeding due to the discrete, ordered nature of these phenotypes. This study presents a novel Bayesian divergence-based framework for multitrait ordinal selection, implemented in the extended Multitrait Parental Selection R package (MPS-R). By leveraging decision-theoretic loss functions, including the Kullback-Leibler (KL) divergence, Bhattacharyya distance, and Hellinger distance, our approach quantifies the distance between candidate distributions and breeder-defined target distributions. Through extensive simulations under 6 scenarios combining different genetic correlation structures and heritability levels, we demonstrate the comparative performance of each loss function. KL divergence consistently yielded superior genetic gains, especially in moderate heritability settings. Additionally, random sampling validation using real wheat disease resistance data confirmed the utility of these methods in practical breeding contexts. The MPS-R package implements this methodology through user-friendly functions tailored for ordinal trait selection in breeding applications. Our results demonstrate that this toolset provides a flexible, robust, and biologically grounded framework to enhance selection efficiency in breeding programs targeting complex, multitrait ordinal phenotypes. A couple of limitations employed by the simulation scheme used on the study are also discussed.</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/PMC12506649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949090","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":"Grizzly bear population genomics across a coastal-interior ecotone in British Columbia, Canada.","authors":"Lauren H Henson, Kris A Christensen, Ben J G Sutherland, Hollie A Johnson, Bridgett vonHoldt, Astrid Vik Stronen, Paul Paquet, Jason Moody, Ben F Koop, Chris T Darimont","doi":"10.1093/g3journal/jkaf237","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf237","url":null,"abstract":"<p><p>Local adaptation research often focuses on discrete populations without extensive gene flow that are under differential selective pressures. By contrast, grizzly bears Ursus arctos in British Columbia (BC) are wide-ranging omnivores that span an environmental and resource ecotone from the coastal, salmon-enriched rainforest to dry interior plateau. This ecotone has been associated with local adaptation in other species and the different regions to morphological variation in grizzly bears. To understand genome-wide population genetic patterns across the ecotone and to identify loci or genomic regions associated with these different environments, here we use whole-genome resequencing to characterize 3.9 M SNPs in 31 grizzly bears spanning central to northern latitudes in coastal and interior regions (to the west and east of the Coastal Mountain Range (CMR), respectively). Clustering grizzly samples by genotypes identified three groups that generally correspond to the source geographic regions, with the greatest variation occurring from north to south. The data were best explained by a single ancestry cluster, but K = 3 recovered the three geographic groupings and was used to identify putative non-migrant individuals. The presence of individuals with mixed ancestry (using K = 3) provides evidence for travel across the CMR, but significant differentiation between clusters (mean FST = 0.015-0.036) suggests some genetic separation between the regions, supporting an isolation-by-distance or clinal variation model. Putative close-kin were identified and removed, then multiple supervised outlier SNP detection methods were applied to identify regions of the genome consistently segregating between coastal and interior regions. Several associated genomic regions and candidate genes were identified, including a consistently identified outlier region near the gene creatine kinase, m-type. This work provides the first genome-wide analysis of grizzly bears in the studied region. These findings will be useful for connectivity planning and research on the adaptability of coastal and interior grizzlies to future climate change scenarios.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238454","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":"De novo genome assembly of the endemic Italian springtail Orchesella dallaii (Collembola: Orchesellidae).","authors":"Claudio Cucini, Francesco Nardi, Rebecca Funari, Riccardo Bulletti, Antonio Carapelli, Pietro Paolo Fanciulli, Francesco Frati","doi":"10.1093/g3journal/jkaf240","DOIUrl":"https://doi.org/10.1093/g3journal/jkaf240","url":null,"abstract":"<p><p>Springtails (Collembola) constitute one of the most diverse and ecologically important groups of basal hexapods, yet remain significantly underrepresented in genomic databases. In this study, we present the first genome assembly of Orchesella dallaii, an Italian endemic species, representing a crucial advancement in expanding genomic resources for Collembola. Utilizing PacBio HiFi sequencing combined with an ultra-low input library preparation, we generated a highly contiguous genome assembly (223 contigs covering 304Mb) that ranks among the most complete ones within the group. Genome annotation, supported by short-read RNA-seq data, predicted 31,769 genes with high completeness. The analysis of repeated sequences revealed a comparatively low abundance of annotated transposable elements. Additionally, the entire mitochondrial genome was assembled and annotated, confirming the gene order characteristic of the Entomobryomorpha lineage. This genomic resource provides a valuable reference for an often-overlooked taxonomic group and offers a basis for future research in comparative genomics, species delimitation, and conservation genetics of Mediterranean soil ecosystems.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145238472","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}