G3: Genes|Genomes|Genetics最新文献_第8页

Identification of novel inhibitors of Mycobacterium smegmatis growth through genome-wide overexpression of Cluster P3 mycobacteriophage Xavia genes. 通过P3簇噬菌体Xavia基因的全基因组过表达鉴定耻垢分枝杆菌生长的新型抑制剂。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-16 DOI: 10.1093/g3journal/jkag262

Anushka Tennakoon, Iresha K Edirisingha, Cole R Jirsa, Ethan Rutledge, Ankita Bhattacharyya, Ella King, Madelyn Moresi, Amara Lovings, Parker R Yarborough, Anna Hoben, Garrett Manns, Toney Ray Gibson, Syed Mohammed Ashfaque Uddin, Yeseul Bae, Natalie Taylor, Taylor L Johnson, Madelyn Futral, Paige Wilson, Jalyn Brown, Zackari L Arbogast, Abigail Brooks, Carson Ward, Courtney Foxworth, Kacey Nguyen, Daphne Fairchild, Deisy Lemus, Hayley White, Holly Craft, Justin Adonis, Kamiya Givan, Sergio Valdivia, Kayci Beth Wallace, Madeline Bent, Shikelya D Chambliss, Dmitri Mavrodi, Danielle M Heller, Ramesh Rijal

{"title":"Identification of novel inhibitors of Mycobacterium smegmatis growth through genome-wide overexpression of Cluster P3 mycobacteriophage Xavia genes.","authors":"Anushka Tennakoon, Iresha K Edirisingha, Cole R Jirsa, Ethan Rutledge, Ankita Bhattacharyya, Ella King, Madelyn Moresi, Amara Lovings, Parker R Yarborough, Anna Hoben, Garrett Manns, Toney Ray Gibson, Syed Mohammed Ashfaque Uddin, Yeseul Bae, Natalie Taylor, Taylor L Johnson, Madelyn Futral, Paige Wilson, Jalyn Brown, Zackari L Arbogast, Abigail Brooks, Carson Ward, Courtney Foxworth, Kacey Nguyen, Daphne Fairchild, Deisy Lemus, Hayley White, Holly Craft, Justin Adonis, Kamiya Givan, Sergio Valdivia, Kayci Beth Wallace, Madeline Bent, Shikelya D Chambliss, Dmitri Mavrodi, Danielle M Heller, Ramesh Rijal","doi":"10.1093/g3journal/jkag262","DOIUrl":"https://doi.org/10.1093/g3journal/jkag262","url":null,"abstract":"Bacteriophages encode numerous genes with no known function, many of which can affect essential cellular processes when expressed in the bacterial host. For mycobacteriophages, genome-wide overexpression in Mycobacterium smegmatis can be used to identify proteins that impair growth. To evaluate the cytotoxic potential of the Cluster P3 phage Xavia, we constructed a plasmid library containing 71 predicted Xavia genes under the anhydrotetracycline inducible promoter pTet and screened this library in a plate-based cytotoxicity assay to measure impacts on M. smegmatis growth. Two genes prevented transformants recovery, consistent with toxicity under basal promoter leakiness, and inducible expression of 18 additional genes impaired growth. These inhibitory proteins include structural components; factors involved in DNA metabolism, lysogeny, and lysis; and several proteins with no known function. These results extend functional screening into a lineage of actinobacteriophages that has not previously been characterized, and identify new proteins that warrant further mechanistic analysis.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148982547","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}

引用次数: 0

Draft genome assembly of the green-bronze dung beetle, Onthophagus orpheus. 绘制绿青铜屎壳虫（Onthophagus orpheus）基因组组装图。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-16 DOI: 10.1093/g3journal/jkag256

Alexander J Bradshaw, Javier F Tabima, Erin L McCullough

引用次数: 0

Chromosome-level genome assembly of the bitterling Rhodeus sinensis (Acheilognathidae) reveals genomic signatures associated with its mussel-dependent reproductive system. 苦味中华罗迪斯（halilognathidae）的染色体水平基因组组装揭示了与其依赖贻贝的生殖系统相关的基因组特征。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-12 DOI: 10.1093/g3journal/jkag260

Rawon Jeong, Jeonghun Kim, Ho Young Suk

{"title":"Chromosome-level genome assembly of the bitterling Rhodeus sinensis (Acheilognathidae) reveals genomic signatures associated with its mussel-dependent reproductive system.","authors":"Rawon Jeong, Jeonghun Kim, Ho Young Suk","doi":"10.1093/g3journal/jkag260","DOIUrl":"https://doi.org/10.1093/g3journal/jkag260","url":null,"abstract":"Bitterlings (Acheilognathidae) exhibit a unique reproductive strategy characterized by symbiotic embryonic development inside the gill cavities of freshwater unionid mussels. Despite extensive ecological and physiological research on this system, genomic resources for bitterlings have remained limited, hindering comparative and evolutionary studies. Here, we present a high-quality, chromosome-level genome assembly for Rhodeus sinensis, a widely distributed bitterling species in the Korean Peninsula. By combining PacBio Continuous Long Read (CLR) sequencing, Illumina short reads, and Hi-C scaffolding, we generated a 0.77 Gb genome assembly with a scaffold N50 of 30.06 Mb. The final assembly comprises 24 chromosome-scale scaffolds, accounting for 98.3% of the assembled genome, with a BUSCO completeness score of 96.3% against the Actinopterygii_odb10. Comparative genomic analyses identified prominent expansions in gene families associated with alcohol metabolism, lipid catabolism, and oxidative stress responses. These genomic signatures of metabolic rewiring suggest a potential fuel flexibility, which may serve as a critical adaptive mechanism to mitigate the severe hypoxic stress encountered within the host mussel's gill environment. Ultimately, our chromosome-level genome assembly and findings provide a robust genomic foundation, contributing to a deeper understanding of the extreme physiological adaptations and unique life-history evolution within the Acheilognathidae.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148955451","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}

引用次数: 0

Digital Kennison: A bioinformatics pipeline for rapid mapping of sequences to the Drosophila melanogaster Y chromosome. 数字Kennison：用于快速绘制黑腹果蝇Y染色体序列的生物信息学管道。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-10 DOI: 10.1093/g3journal/jkag253

Fabiana Uno, A Bernardo Carvalho

{"title":"Digital Kennison: A bioinformatics pipeline for rapid mapping of sequences to the Drosophila melanogaster Y chromosome.","authors":"Fabiana Uno, A Bernardo Carvalho","doi":"10.1093/g3journal/jkag253","DOIUrl":"https://doi.org/10.1093/g3journal/jkag253","url":null,"abstract":"The Drosophila melanogaster Y chromosome is currently known to contain 13 single-copy protein-coding genes, six of which are essential for male fertility, as well as several non-coding genes and abundant repetitive DNA. Localization of Y-linked sequences has traditionally relied on labor-intensive crosses using Kennison's translocation strains, which map Y-linked loci by generating flies deficient for each of the six Y-chromosome fertility regions (ks-1, ks-2, kl-1, kl-2, kl-3, and kl-5). Here we present Digital Kennison, a computational pipeline that recasts this classical mapping strategy as a sequence-based analysis. The pipeline queries eight genomic databases derived from Kennison's strains using BLAST and read coverage, assigning sequences to fertility regions or the centromeric region with a calibrated confidence score. We benchmarked the method on 60 Y-linked sequences spanning all seven regions, including single-copy protein-coding genes, Mst77Y family members, non-coding RNAs, and the centromere. Digital Kennison achieved 97% precision while resolving challenging cases, including boundary-spanning genes (PRY and Ppr-Y), fragmented Mst77Y copies, and FDY, which has a closely related autosomal paralog. Beyond validating known localizations, the pipeline localized the unmapped gene CG41561 to the kl-1region and reassigned the transcript CR40629-RC from the kl-2 region to kl-5. It also localized 7 of 16 recently transferred Y-linked sequences, including 4 with high confidence. Applied to 904 R6 scaffolds, Digital Kennison assigned 75% to fertility regions, including five currently annotated as autosomal-pericentromeric. Digital Kennison reduces sequence localization from weeks of genetic crosses to minutes of computation while preserving the power of classical translocation mapping.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148929581","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}

引用次数: 0

Spore type-specific gene expression profiles underlying development and leaf infection processes of Colletotrichum graminicola. 禾本科炭疽病菌发育和叶片侵染过程中孢子型特异性基因表达谱。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-09 DOI: 10.1093/g3journal/jkag254

Disha Rathi, Karsten Andresen, Rolf Daniel, Marco Alexandre Guerreiro, Matthias Kretschmer, James Kronstad, Minou Nowrousian, Stefanie Pöggeler, Anja Poehlein, Lars M Voll, Daniela Elisabeth Nordzieke

{"title":"Spore type-specific gene expression profiles underlying development and leaf infection processes of Colletotrichum graminicola.","authors":"Disha Rathi, Karsten Andresen, Rolf Daniel, Marco Alexandre Guerreiro, Matthias Kretschmer, James Kronstad, Minou Nowrousian, Stefanie Pöggeler, Anja Poehlein, Lars M Voll, Daniela Elisabeth Nordzieke","doi":"10.1093/g3journal/jkag254","DOIUrl":"https://doi.org/10.1093/g3journal/jkag254","url":null,"abstract":"Colletotrichum graminicola causes significant losses of the staple crop maize worldwide. The fungus produces two distinct asexual spore types, oval and falcate conidia, which show unique processes in development and plant interaction. Based on genome resequencing of our laboratory strain (CgM2/M1.001), we investigated the gene expression profiles of oval and falcate conidia during development and early leaf infection using RNA-seq. Our results reveal specific gene expression profiles between the two spore types, indicating fundamental differences in their developmental programs that reflect different modes of infection. We identified expression patterns discriminating both conidia types from mycelium and spore type-specific ones for genes encoding transcription factors, conserved fungal developmental genes, transporters, genes of secondary metabolite clusters, and pathogenicity-related functions, including effectors and carbohydrate-active enzymes (CAZymes). Our study shows that despite the identical genomic basis, oval and falcate conidia show unique transcriptomes across vegetative development and early plant interaction. Taking together, these results provide new insights into the molecular mechanisms determining the biology of C. graminicola and its interaction with the plant host.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918942","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}

引用次数: 0

Seasonal fluctuations in fitness result in severe reductions in effective population size. 适应度的季节性波动导致有效种群规模的严重减少。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-03 DOI: 10.1093/g3journal/jkag252

Olivia L Johnson, Raymond Tobler, Joshua M Schmidt, Christian D Huber

{"title":"Seasonal fluctuations in fitness result in severe reductions in effective population size.","authors":"Olivia L Johnson, Raymond Tobler, Joshua M Schmidt, Christian D Huber","doi":"10.1093/g3journal/jkag252","DOIUrl":"10.1093/g3journal/jkag252","url":null,"abstract":"Genetic evidence for fluctuating selection has begun to accumulate for different species over the past few decades, especially for the Drosophila genus where studies have reported hundreds of loci undergoing putatively adaptive oscillations across successive seasons. However, most theoretical and simulation studies of fluctuating selection have relied on abstract or weakly parameterized models, making it difficult to assess their relevance for natural populations. In this study, we simulate multilocus seasonally fluctuating selection acting on standing genetic variation under a recently developed model and examine its effect on the variance effective population size (Ne) at a genome-wide scale. By recapitulating genomic, demographic, and evolutionary parameters from natural Drosophila populations in our simulations, we were able to reproduce allele frequency oscillations reported in recent studies and show that these lead to ∼50% genome-wide reductions in Ne. We also demonstrate that Ne reductions are well predicted by the maximum frequency amplitude among all adaptively fluctuating loci, and that the frequency amplitudes are largely determined by the number of adaptively fluctuating loci and the strength of their epistatic interactions. Our results demonstrate that fluctuating selection can substantially reduce effective population size and underscore the importance of temporally variable selection in shaping genome-wide patterns of variation beyond classical models.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886925","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}

引用次数: 0

Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes. 地衣真菌富含helitron，代长长，分布尺寸小。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-02 DOI: 10.1093/g3journal/jkag153

Julianna Paulsen, Stephen T Sharrett, Devin Mumey, Elaine M Larsen, Nguyen Khoi Nguyen, James Lendemer, Lalita M Calabria, Jordan R Hoffman, Krisztian Magori, Jessica L Allen

{"title":"Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes.","authors":"Julianna Paulsen, Stephen T Sharrett, Devin Mumey, Elaine M Larsen, Nguyen Khoi Nguyen, James Lendemer, Lalita M Calabria, Jordan R Hoffman, Krisztian Magori, Jessica L Allen","doi":"10.1093/g3journal/jkag153","DOIUrl":"10.1093/g3journal/jkag153","url":null,"abstract":"Transposable elements have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read-based metagenomically assembled reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publicly available genomes to investigate the relationships between species traits (i.e. dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of transposable elements using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradict previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of transposable elements in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater transposable element activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving transposable element proliferation in rare species' genomes and if transposable element content is predictive of increased extinction risk.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257697","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}

引用次数: 0

Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation. 栽培葡萄的全基因组分析证实了高基因组共线性和广泛的可有可无的基因含量可能参与适应。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-02 DOI: 10.1093/g3journal/jkag168

Baptiste Pierre, Roberto Bacilieri, Dominique This, Thierry Lacombe, Vincent Segura, Patrice This, Anne Mocoeur, Romain Villoutreix, Gautier Sarah

{"title":"Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.","authors":"Baptiste Pierre, Roberto Bacilieri, Dominique This, Thierry Lacombe, Vincent Segura, Patrice This, Anne Mocoeur, Romain Villoutreix, Gautier Sarah","doi":"10.1093/g3journal/jkag168","DOIUrl":"10.1093/g3journal/jkag168","url":null,"abstract":"Pangenomes have now been developed for several horticultural crops, yet the extent to which genome diversity in sequence and organization contribute to plant adaptation and major agronomic traits remains poorly understood. Here, we assembled the genomes of 9 cultivated grapevine varieties and compared the genomes of 15 cultivated grapevine varieties for variation in gene and TE content. We found that genomic collinearity is highly conserved among varieties. We still observed substantial variation across genomes. Notably, we identified across varieties 55,662 orthologous genes, of which 55.3% appears to be dispensable. Dispensable genes are enriched for functions related to adaptation to biotic and abiotic constraints, suggesting that they may play a role in adaptation. Comparing our results with a recently published study, we found substantial differences with ∼12.6% of the genes we classified as core genes being classified as dispensable genes in this other study. We then constructed a pangenome graph and used it to performed genome-wide association studies for 3 important traits in grapevine production, which allowed us to include large structural variants as markers in the analyses. We identified 32 loci that we did not detect when we used the PN40024 genome as a reference, 20 of which are newly reported associations. Overall, our results indicates that despite recent advances in characterizing plant pangenomes, current gene classification into core and dispensable gene categories should be taken with caution. They also highlight the value of incorporating structural variants into GWAS, to better characterize the genetic architecture of agronomic traits.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13535373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148411024","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}

引用次数: 0

Temporal transcriptomic and microbiome changes in American bison during experimental SARS-CoV-2 challenge. 美国野牛在实验性SARS-CoV-2挑战期间的时间转录组学和微生物组变化

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-02 DOI: 10.1093/g3journal/jkag231

Bruna Petry, Paola M Boggiatto, Alexandra Buckley, Eric D Cassmann, Kaitlyn Sarlo Davila, Steven C Olsen, Luis Guilherme Virgilio Fernandes, Bienvenido Tibbs-Cortes, Faith M Rahic-Seggerman, Mitchell V Palmer, Ellie J Putz

{"title":"Temporal transcriptomic and microbiome changes in American bison during experimental SARS-CoV-2 challenge.","authors":"Bruna Petry, Paola M Boggiatto, Alexandra Buckley, Eric D Cassmann, Kaitlyn Sarlo Davila, Steven C Olsen, Luis Guilherme Virgilio Fernandes, Bienvenido Tibbs-Cortes, Faith M Rahic-Seggerman, Mitchell V Palmer, Ellie J Putz","doi":"10.1093/g3journal/jkag231","DOIUrl":"https://doi.org/10.1093/g3journal/jkag231","url":null,"abstract":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a threat to humans as well as domestic and wild animals. The variability in severity of clinical signs, the zoonotic potential, and the host-specific response to infection contribute to the persistence of circulation of disease. In wildlife species, white-tailed deer have been shown to be more permissive to infection than bovids. However, among bovids, American bison have shown a greater susceptibility than cattle. In this study, we investigate the transcriptomic response to experimental SARS-CoV-2 infection in bison over time. Substantial numbers of differentially expressed genes were identified between pre- and 2, 5, 7, 14, and 21 days post-inoculation. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology term analysis identified associations with immune response, inflammatory response, and viral infection including COVID-19. Ingenuity Pathway Analysis of the coronavirus pathway highlighted differences in signaling at days 2 versus 21 post-inoculation. We additionally examined changes in the nasal microbiome of bison over the course of experimental infection, which suggested an increase in opportunity for secondary infection causing pathogens such as Mannheimia. Collectively, this study presents a profile of bison transcriptomic response to SARS-CoV-2 infection and continues to expand our understanding of variation in host response.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148879829","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}

引用次数: 0

Leveraging human-trained neural networks for cross-species chromatin regulation annotations. 利用人类训练的神经网络进行跨物种染色质调控注释。

IF 2.4 3区生物学

G3: Genes|Genomes|Genetics Pub Date : 2026-09-02 DOI: 10.1093/g3journal/jkag230

Noémien Maillard, Julie Demars, Raphaël Mourad

{"title":"Leveraging human-trained neural networks for cross-species chromatin regulation annotations.","authors":"Noémien Maillard, Julie Demars, Raphaël Mourad","doi":"10.1093/g3journal/jkag230","DOIUrl":"https://doi.org/10.1093/g3journal/jkag230","url":null,"abstract":"Analogous to the Encyclopedia of DNA Elements (ENCODE) project, the Functional Annotation of ANimal Genomes (FAANG) consortium has produced chromatin annotations for domesticated animals, albeit in smaller amounts. Although acquiring experimental data is more accessible and affordable for many species, human and mouse organisms will remain the reference. Classical methods based on sequence conservation can be used to infer missing annotations, but are inappropriate for non-conserved sequences. While regulatory sequences share low to moderate conservation, they have retained their regulatory function during the evolution process. Here, we take advantage of three neural networks (DeepBind, DeepSEA, and Enformer) trained with human and mouse ENCODE data to infer chromatin annotations (transcription factors binding, chromatin accessibility, and histone marks) in cattle, pig, chicken, and European seabass. For this purpose, we comprehensively assessed the quality of predictions using experimental data from FAANG, through AUC-ROC and AUC-PR metrics. Our results showed low variability between tissues and similar performances for various annotations in mammals and chicken, with AUC-PR ranging from 0.663 ± 0.010 (chicken) to 0.765 ± 0.009 (pig) for the best predicted experiment, H3K4me3 (all tissues grouped), but lower (0.238 ± 0.005) in fish. Further analyses focused on pigs highlighted (i) accurate predictions even for non-conserved sequences, and (ii) variable predictions depending on genomic feature annotations. Our results advocate the widespread use of human-trained neural networks as a first step in cross-species genome annotation before training species-specific models.","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148873548","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}

引用次数: 0