Genome最新文献 - Book学术

Feature selection and dimensionality reduction in multi-omics. 多组学的特征选择与降维。

IF 1.9 3区生物学

Genome Pub Date : 2026-10-18 DOI: 10.1139/gen-2026-0094

Sweta Rai, Igor Kovalchuk

{"title":"Feature selection and dimensionality reduction in multi-omics.","authors":"Sweta Rai, Igor Kovalchuk","doi":"10.1139/gen-2026-0094","DOIUrl":"https://doi.org/10.1139/gen-2026-0094","url":null,"abstract":"High-throughput multi-omics technologies generate high-dimensional, heterogeneous and noisy datasets, making robust biomarker discovery and disease modelling challenging. This review critically examines dimensionality reduction and representation strategies for multi-omics analysis while distinguishing three related but different goals: feature selection, feature extraction/representation learning, and multi-omics integration. We use sparse canonical correlation analysis (sCCA), variational autoencoders (VAEs), and graph convolutional networks (GCNs) as representative case studies spanning sparse linear, probabilistic deep-learning, and graph-based approaches. Rather than treating these methods as interchangeable, we compare their data requirements, assumptions, interpretability, ability to accommodate non-linearity and missing modalities, computational demands, and validation needs. Applications across cancer, cardiovascular and neurodegenerative disease, and across bulk, single-cell, spatial and imaging multi-omics are summarized in comparative tables. We conclude with practical guidance for matching method families to biological questions and emphasize that robust biomarker claims require leakage-free model development, stability assessment and independent validation.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220386","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

Lipid requirements for brain development and function: what we can learn from Drosophila melanogaster. 脑发育和功能的脂质需求：我们可以从黑腹果蝇那里学到什么。

IF 1.9 3区生物学

Genome Pub Date : 2026-10-18 DOI: 10.1139/gen-2026-0087

Karen He, Madeleine Margaret Dee, Andrew J Simmonds

引用次数: 0

Cross-sector partnership and DNA barcoding to boost biological knowledge in megadiverse countries. 跨部门伙伴关系和DNA条形码促进生物多样性大国的生物知识。

IF 1.9 3区生物学

Genome Pub Date : 2026-10-17 DOI: 10.1139/gen-2026-0024

Juan Alejandro Guerrero-Cupacán, Eduardo Tovar Luque, Julian Clavijo-Bustos, Jose Vladimir Sandoval-Sierra, Gustavo Aristizabal-H, Diego Fernando Puentes Mojica, Maria Juliana Salcedo Hernández, Viviana Buitrago, Xiomara Sanclemente Manrique, Mailyn Gonzalez

{"title":"Cross-sector partnership and DNA barcoding to boost biological knowledge in megadiverse countries.","authors":"Juan Alejandro Guerrero-Cupacán, Eduardo Tovar Luque, Julian Clavijo-Bustos, Jose Vladimir Sandoval-Sierra, Gustavo Aristizabal-H, Diego Fernando Puentes Mojica, Maria Juliana Salcedo Hernández, Viviana Buitrago, Xiomara Sanclemente Manrique, Mailyn Gonzalez","doi":"10.1139/gen-2026-0024","DOIUrl":"https://doi.org/10.1139/gen-2026-0024","url":null,"abstract":"Global biodiversity loss requires efforts from all sectors to preserve what may be last refuges for species in transformed ecosystems. Furthermore, robust DNA reference libraries are essential for advancing future biodiversity monitoring. However, huge gaps remain, particularly in tropical regions. We conducted rapid biodiversity inventories in four Voluntary Corporate Conservation Areas in Colombia (VCCA) that seek to combine oil operations while preserving biodiversity. Our approach combined strategic sequencing prioritization of vertebrates, plants, and focal arthropods to close genetic knowledge gaps, with a systematic Malaise-trap experiment to assess arthropod richness and turnover using cost-effective MinION sequencing. This industry-enabled effort generated 5037 barcodes representing 2517 taxonomic entities. Arthropod BIN-based analyses revealed high richness and turnover among localities and land covers. Notably, 42.4% of the sequences were new to BOLD, expanding reference data and existing public records for these regions by two- to nine-fold. MinION processing reduced per-sample sequencing costs from USD 6.25-10.41 to ~USD 0.65, providing a scalable and cost-effective strategy to inventory 'dark taxa'. Our results set the base for further biodiversity planning by the industry in their operational area and illustrate that industry-enabled molecular workflows can accelerate biodiversity knowledge and provide reference data for future applications such as DNA-based monitoring.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149216194","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

Insights into plant LINE evolution: Essential domains persist amidst widespread structural degeneration. 植物LINE进化的见解：基本结构域在广泛的结构退化中持续存在。

IF 1.9 3区生物学

Genome Pub Date : 2026-10-06 DOI: 10.1139/gen-2026-0080

Thamirys Silva Valentim, Lucas Johnen, Juliana Machado da Silva, Matheus Pimenta, Guilherme Borges, Leticia Maria Parteka, Rafael de Assis, André Marques, Fabricio Martins Lopes, André Laforga Vanzela

{"title":"Insights into plant LINE evolution: Essential domains persist amidst widespread structural degeneration.","authors":"Thamirys Silva Valentim, Lucas Johnen, Juliana Machado da Silva, Matheus Pimenta, Guilherme Borges, Leticia Maria Parteka, Rafael de Assis, André Marques, Fabricio Martins Lopes, André Laforga Vanzela","doi":"10.1139/gen-2026-0080","DOIUrl":"https://doi.org/10.1139/gen-2026-0080","url":null,"abstract":"Plant long interspersed nuclear elements (LINEs) are structurally diverse, experience periodic pulses of degeneration, and occur in lower copy numbers than LTR retrotransposons. Consequently, their macroevolutionary dynamics remain poorly understood. Here, we curated a high-stringency reverse transcriptase (RT) database to annotate structurally complete LINEs across 54 plant genomes spanning from Marchantiopsida to Magnoliopsida. The highly selective filtering yielded a refined dataset dominated by L1 and RTE families, whereas I, R2, and Jockey superfamilies were rare and highly degenerate. Full-length elements retained at least essential ORF2 domains (EEP and RT) alongside a 3' poly(A) tail. However, those of longer length exhibited structural variability, carrying 5' ORF1 regions, non-essential ORF2 domains (Zf-RVT and RNH), and, in some cases, 3' (GTT)n motifs before the poly(A) tail. L1 elements were larger and showed greater EEP-RT domain heterogeneity than RTE. Nonetheless, RT-based phylogeny robustly separated these two groups. An alignment-free k-mer-based pipeline (k = 9) validated our manual annotations and successfully resolved degraded domains and interstitial gaps missed by conventional BLAST alignments. Furthermore, genomic abundance showed only a moderate positive correlation with genome size, underscoring lineage-specific TE dynamics. Overall, our findings demonstrate that plant LINE evolution is driven by widespread structural degeneration, where the selective persistence of core catalytic domains (RT and EEP) sustains element survival amidst extensive domain loss across land plants.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108805","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

Integration of cytogenetics and genomics reveals translocation and recombination between nonhomologous chromosomes in a novel wheat line with dual introgression. 结合细胞遗传学和基因组学，揭示了一个具有双渗入的小麦新品系的非同源染色体之间的易位和重组。

IF 1.9 3区生物学

Genome Pub Date : 2026-10-03 DOI: 10.1139/gen-2025-0129

Weiwei Song, Tong Zhou, Qianyu Xing, Yaqi Bao, Liangyu Zhu, Xinyu Zhao, Yunfeng Qu, Yimeng Xu, Changtong Jiang, Xinling Li, Xuanzhao Li, Lei Cui, Hongjie Li, Fei He, Yanming Zhang

{"title":"Integration of cytogenetics and genomics reveals translocation and recombination between nonhomologous chromosomes in a novel wheat line with dual introgression.","authors":"Weiwei Song, Tong Zhou, Qianyu Xing, Yaqi Bao, Liangyu Zhu, Xinyu Zhao, Yunfeng Qu, Yimeng Xu, Changtong Jiang, Xinling Li, Xuanzhao Li, Lei Cui, Hongjie Li, Fei He, Yanming Zhang","doi":"10.1139/gen-2025-0129","DOIUrl":"https://doi.org/10.1139/gen-2025-0129","url":null,"abstract":"The development of wheat-rye-Thinopyrum hybrids is a key strategy for introgressing agronomically valuable traits from multiple genera into common wheat, enriching its genetic diversity. However, the labor-intensive and time-consuming identification of lines carrying chromatin segments from all three donors has limited its widespread application. In this study, a stable hexaploid wheat line, 13-26 (2n=6x=42, AABBDD, T6JvsS·6AL-T5R·2D-T5R·4B), was developed by crossing octoploid Trititrigia with hexaploid triticale, followed by 17 generations of self-pollination. Line 13-26 outperforms its parents agronomically, with well-filled kernels and a TKW exceeding both parental lines, and the higher protein content relative to the male parent. Analyses via smGISH, mcFISH, and short-read sequencing confirmed the integration of wheat, rye, and Thinopyrum chromatin. Approximately 220 Mb was absent from wheat chromosome 6AS and 89 Mb from 2DL, while around 221 Mb of Thinopyrum 6JvsS and 42 Mb of rye 5RL were detected. Line 13-26 carries a Th. intermedium T6JvsS·6AL translocation and terminal segments of rye 5RL translocated to wheat 2DL and 4BL, demonstrating intergeneric translocation and recombination between nonhomologous chromosomes, which represents a valuable germplasm resource with integrated multi-genus traits. This combined cytogenomic approach enhances the sensitivity and specificity of alien chromatin detection, providing a robust framework for characterizing complex chromosomal rearrangements in polyploid wheat.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108853","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

Phylogeny and ecosystem jointly shape metabolite sensing by structured noncoding RNAs. 系统发育和生态系统共同塑造了结构化非编码rna对代谢物的感知。

IF 1.9 3区生物学

Genome Pub Date : 2026-09-28 DOI: 10.1139/gen-2026-0048

Senthilkumar Kailasam, Rashmi Rekha Panigrahi

{"title":"Phylogeny and ecosystem jointly shape metabolite sensing by structured noncoding RNAs.","authors":"Senthilkumar Kailasam, Rashmi Rekha Panigrahi","doi":"10.1139/gen-2026-0048","DOIUrl":"https://doi.org/10.1139/gen-2026-0048","url":null,"abstract":"Non-coding RNAs (ncRNAs) regulate gene expression through diverse structural and sequence-based mechanisms, often acting without protein intermediates. Riboswitches are cis-regulatory ncRNAs that directly sense small molecule metabolites to control gene expression. Many riboswitches operate through kinetic control, meaning the rate at which a ligand binds to the aptamer domain determines whether gene expression is turned ON or OFF. Here, we present a comparative survey of riboswitch repertoires across eight microbiomes: human gut, oral, skin, vaginal, mouse gut, pig gut, sheep rumen, and marine environment, spanning 13,946 prokaryotic genomes. Using covariance models, we identified 86,485 riboswitches across 12,916 genomes (92.6%), representing 23 metabolite-sensing classes, with six dominant classes accounting for ~70% of all riboswitch hits. Riboswitch composition varied significantly across ecosystems, but variance partitioning showed this structure is driven primarily by phylogeny: phylum explained 25.5% of compositional variance, whereas the fraction uniquely attributable to ecosystem after conditioning on taxonomy, was only 2.2%. Overall riboswitch distributions reflect both phylogenetic and ecological influences, highlighting their role in shaping metabolite-responsive regulatory strategies across microbial life.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149074471","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

Environmental DNA for detecting marine fish species: testing the volume of sampled water, markers and primers in a public oceanarium. 用于检测海洋鱼类的环境DNA：在公共海洋馆中测试取样水、标记物和引物的体积。

IF 1.9 3区生物学

Genome Pub Date : 2026-09-27 DOI: 10.1139/gen-2026-0026

André O Ferreira, Cláudia Machado, Cristina Barroso, Núria Baylina, Conceição Egas, João T Fontes, Margarida Fernandes, Claudio Oliveira, A Miguel Piecho-Santos, Sofia Duarte, Filipe Oliveira Costa

{"title":"Environmental DNA for detecting marine fish species: testing the volume of sampled water, markers and primers in a public oceanarium.","authors":"André O Ferreira, Cláudia Machado, Cristina Barroso, Núria Baylina, Conceição Egas, João T Fontes, Margarida Fernandes, Claudio Oliveira, A Miguel Piecho-Santos, Sofia Duarte, Filipe Oliveira Costa","doi":"10.1139/gen-2026-0026","DOIUrl":"https://doi.org/10.1139/gen-2026-0026","url":null,"abstract":"To maximize the efficiency of marine fish detection using environmental DNA (eDNA) metabarcoding, methodological factors such as PCR amplification bias and sampled water volume must be carefully considered. In this study, we evaluated the influence of different genetic markers (COI, 12S rRNA, and 16S rRNA) and water sample volumes (0.5, 1.0, 2.5, 5.0, and 10 L) on eDNA-based detection of 60 marine fish species maintained at the Oceanário de Lisboa. Five primer sets were used to generate amplicon libraries from triplicate water samples per tested volume. Overall, the combined use of all markers enabled the detection of 81.7% of the fish species present in the tank (n=49), as well as 37 additional exogenous taxa. Detection success varied among primer sets, ranging from 31.7% for COI FishATL_Cocktail1 to 73.3% for Fish16S. When accounting for reference sequence availability, relative detection success reached 82.4% for 12S and 77.2% for 16S. Increasing water volume consistently led to higher species detection across all markers, with detection percentages approaching saturation at the highest volumes tested. When pooling all markers, up to 76.7% of the species present were detected using a water volume of 5 L. These results highlight the limitations of relying on a single genetic marker and demonstrate the strong influence of sampling volume on detection efficiency, a factor likely to be even more critical in open marine environments.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069472","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

Genotype dependent microbial community restructuring under salinity stress outweighs direct benefits of native microbe inoculation in Hordeum vulgare. 盐胁迫下基因型依赖的微生物群落重组超过了原生微生物接种的直接效益。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-06 DOI: 10.1139/gen-2025-0095

Jack Walter Lewis Royle, Soudeh Farzadfar, John Paul Wasan, Jonathan Bennett

{"title":"Genotype dependent microbial community restructuring under salinity stress outweighs direct benefits of native microbe inoculation in Hordeum vulgare.","authors":"Jack Walter Lewis Royle, Soudeh Farzadfar, John Paul Wasan, Jonathan Bennett","doi":"10.1139/gen-2025-0095","DOIUrl":"https://doi.org/10.1139/gen-2025-0095","url":null,"abstract":"Soil salinization is an escalating threat to global food security under climate change, necessitating innovative strategies to enhance crop resilience. Native microbial inoculants, sourced from salinity-adapted soils, offer a potential avenue for sustainable agricultural adaptation. Here, we evaluated the effects of saline prairie-derived, AMF-enriched microbial inoculants on the growth of barley (Hordeum vulgare) cultivars under a salinity gradient. Greenhouse trials demonstrated that salinity was the dominant constraint on biomass production, but inoculant identity and genotype significantly influenced plant performance and microbial assembly. Inoculant effects on shoot biomass were heterogeneous, with neutral or negative outcomes predominating under saline conditions. Amplicon sequencing of bacterial, fungal, oomycete, and arbuscular mycorrhizal (AMF) communities revealed that salinity strongly restructured microbial diversity and composition, reducing bacterial and fungal evenness. Genotype and inoculant identity shaped fungal communities, while oomycete responses depended on specific plant-microbe pairings. Model selection confirmed that shoot biomass was primarily explained by salinity, with additional contributions from barley genotype, inoculant identity, and fungal evenness. These results demonstrate that microbial community restructuring under salinity stress outweighs direct benefits of native microbial inoculation, and emphasize that successful microbial interventions in salt-affected soils must account for genotype-specific compatibility and stress-driven community dynamics, rather than assuming universal benefits.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145910813","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

Genome Mining Algorithm for Identifying Identical Repeat Sequences to Enhance DNA-Based Diagnostic Assays. 识别相同重复序列的基因组挖掘算法以增强基于dna的诊断分析。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-05 DOI: 10.1139/gen-2025-0027

Kalepu Rajeswari, Raksha Poojary, Padival Shruptha, Rajesh Muliyar Krishna, Kapaettu Satyamoorthy, Bobby Paul

{"title":"Genome Mining Algorithm for Identifying Identical Repeat Sequences to Enhance DNA-Based Diagnostic Assays.","authors":"Kalepu Rajeswari, Raksha Poojary, Padival Shruptha, Rajesh Muliyar Krishna, Kapaettu Satyamoorthy, Bobby Paul","doi":"10.1139/gen-2025-0027","DOIUrl":"https://doi.org/10.1139/gen-2025-0027","url":null,"abstract":"A pair of primers that can bind at multiple loci across the genome and randomly amplify multiple copies increases the analytical sensitivity of the currently used diagnostic assays. We developed a novel genome mining algorithm to identify short identical repeat sequences (IRSs) dispersed across the genome. The genome mining algorithm for IRS identification can be accessed from the GitHub portal (https://github.com/BPaul-bioinfoLAB/IRS-Finder). Using this algorithm, we have identified the IRS from five pathogens, namely, gammaherpesvirus, vaccinia virus, Mycobacterium tuberculosis, Plasmodium falciparum, and Phytophthora palmivora. In-silico PCR revealed that these IRSs can amplify multiple nonhomologous regions of variable amplicon sizes via three priming combinations. We further performed a polymerase chain reaction assay with an IRS pair identified from M. tuberculosis. Interestingly, the PCR with single IRS amplified multiple non-homologous copies and even more variable sized copies in pair. These results indicate that the IRS-based diagnostic assays can detect pathogens in case of low-concentration DNA during disease progression. The genome mining algorithm can be used as a translation technology platform for developing highly sensitive varieties of PCR, microarray, loop-mediated isothermal amplification, fluorescence in-situ hybridization based diagnostic assays.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905938","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

Revealing gene-metabolite interactions in wheat defenses against Pyrenophora tritici-repentis in resistant and susceptible genotypes. 揭示抗性和易感基因型小麦抗小麦焦裂菌的基因-代谢物相互作用。

IF 1.7 3区生物学

Genome Pub Date : 2026-01-01 DOI: 10.1139/gen-2025-0026

Larissa Carvalho Ferreira, Flavio Martins Santana, Manfred Beckmann, Luis A J Mur

{"title":"Revealing gene-metabolite interactions in wheat defenses against Pyrenophora tritici-repentis in resistant and susceptible genotypes.","authors":"Larissa Carvalho Ferreira, Flavio Martins Santana, Manfred Beckmann, Luis A J Mur","doi":"10.1139/gen-2025-0026","DOIUrl":"10.1139/gen-2025-0026","url":null,"abstract":"Wheat defenses against Pyrenophora tritici-repentis (Ptr), the cause of tan spot disease, are complex and require further characterization. We previously identified two wheat genotypes, Robigus (resistant) and Hereward (susceptible), and characterized their differentially expressed genes (DEGs) and accumulated metabolites (DAMs) following challenge with Ptr. In this study we uncover coordinated shifts in gene expression and metabolism triggered by Ptr. The DEGs and DAMs from each genotype were integrated using regularized canonical correlation analysis, yielding scale-free networks with 69 745 edges in Robigus and 760 433 in Hereward. In Robigus, hub genes were upregulated at 48 and 96 h post-inoculation and included hst2 (encoding hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase 2), located within a QTL for Ptr resistance (QTs.fcu-5D locus), a receptor-like kinase, and a late embryogenesis abundant protein (which play roles in cell wall organization). Pathway enrichment showed significant involvement of catalytic activity, chitinase activity, and cell wall metabolic processes. In contrast, Hereward hub genes were mostly downregulated, except for a hexosyltransferase, with enriched pathways related to energy metabolism, such as ATP binding and phosphorylation. These results suggest that cell wall modifications and chitinase activity are part of an effective defense response against Ptr, whereas costly energetic processes may contribute to tan spot susceptibility.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-10"},"PeriodicalIF":1.7,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714130","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