Biology subjects

Kadoo, N.

Publications and source records attributed to Kadoo, N..

4 recordsLinked to original sources

bioRxiv2026

Integrated Pangenomic and Systems Biology Analyses Reveal the Genomic Basis of Virulence and Adaptation in Bipolaris sorokiniana

Bipolaris sorokiniana is a hemibiotrophic fungal pathogen responsible for foliar and root diseases of cereals, causing annual yield losses of 10-50%. The recurrent breakdown of host resistance and the emergence of fungicide-resistant pathogen populations underscore the urgent need to understand the genomic mechanisms underpinning pathogen adaptation and virulence. Here, we present the first comprehensive species-wide pangenomic and systems-level analyses of B. sorokiniana based on 19 genomes of globally distributed strains. Orthology-based analyses revealed an open pangenome comprising 16,981 orthogroups, partitioned into a conserved core genome (60.8%) and a highly dynamic accessory genome (39.2%), consisting of soft-core (8.5%), shell (19.7%), and cloud (11.0%) compartments. The core genes were predominantly associated with essential cellular and metabolic functions, while the accessory fractions were enriched in regulatory, stress-responsive, and adaptive processes. Secondary metabolite profiling identified 39-54 biosynthetic gene clusters per genome and revealed a largely conserved metabolic repertoire. Gene family evolution analyses revealed an excess of gene loss over expansion, indicating ongoing genome streamlining and lineage-specific adaptation. The core interactome comprised four densely connected functional communities governing genome maintenance, ribosome biogenesis, cellular bioenergetics, and protein translation. Collectively, this study elevates B. sorokiniana research from single-genome analyses to a population-scale analysis, providing vital insights into the evolutionary architecture of pathogenicity, adaptation, and genome diversification. These findings provide a valuable genomic resource for disease surveillance and functional characterization of virulence determinants, as well as the development of durable resistance strategies and next-generation antifungals for sustainable disease management in cereals.

bioinformatics↗

bioRxiv2026

A conserved lncRNA regulates trehalose-glucose homeostasis through direct RNA-RNA interactions

Trehalose is a primary circulating sugar in insects and essential for energy homeostasis, yet its non-coding RNA-based regulatory circuitry remains enigmatic. Here, we characterize a conserved long non-coding RNA, lncRNA1, as a post-transcriptional regulator of trehalose-glucose homeostasis in Lepidoptera. lncRNA1 encodes a structurally stable, pseudoknot-containing transcript that is strongly induced upon trehalose pathway perturbation and exhibits a reciprocal developmental expression pattern relative to the trehalose metabolism enzymes. RNAi-mediated silencing of lncRNA1 in Helicoverpa armigera elevates TPS/TPP and Treh transcript abundance, increases enzyme activities, reduces haemolymph trehalose, raises glucose. This drives broad transcriptomic and metabolomic reprogramming of carbohydrate, lipid, and growth-signalling pathways, resulting in accelerated larval growth. Overexpression of lncRNA1 reverses these phenotypes. Mechanistically, lncRNA1 physically associates with TPS/TPP and Treh mRNAs through evolutionarily conserved sequence motifs, modulating their post-transcriptional dynamics. Targeted deletion of these motifs abolishes regulatory activity and disrupts metabolic homeostasis. This regulatory axis is functionally conserved in Spodoptera frugiperda, validated across loss-of-function, gain-of-function, and cell-based systems. Our findings reveal a conserved lncRNA-based layer of post-transcriptional control over insect energy metabolism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/738560v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@eabc51org.highwire.dtl.DTLVardef@f1aaeforg.highwire.dtl.DTLVardef@d64aforg.highwire.dtl.DTLVardef@14d38e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2026

Genome-wide, evolutionary, and stress-responsive landscape of the Pectin methylesterase gene family in cucumber and muskmelon

Pectin methylesterases (PMEs) are key regulators of plant cell wall remodeling; however, their evolutionary dynamics and stress-responsive roles remain poorly understood in cucurbit crops. This study aimed to systematically characterize the PME gene family in cucumber (Cucumis sativus) and muskmelon (Cucumis melo), addressing how PME diversification, duplication, and regulatory architecture underpin their responses to biotic and abiotic stresses. Using a Hidden Markov Model-based genome-wide screening approach, we identified 52 PME genes in cucumber and 56 in muskmelon, which were classified into Type I and Type II PMEs based on their domain composition. Comparative structural and phylogenetic analyses revealed conserved domain organization but substantial intron-driven structural diversification, resolving PMEs into two major evolutionary lineages with lineage-specific expansion patterns. Duplication and synteny analyses demonstrated that dispersed duplication was the primary driver of PME family expansion, while Ka/Ks estimates indicated strong purifying selection, highlighting functional conservation across cucurbits. Promoter cis-element profiling and protein-protein interaction network analyses revealed extensive enrichment of stress- and hormone-responsive regulatory features, identifying central PME hub genes. Meta-transcriptomic analyses across diverse biotic and abiotic stresses revealed dynamic, condition-specific PME regulation, with Type I PMEs predominantly associated with stress responses in cucumber, whereas both PME types contributed substantially in muskmelon. Several PMEs exhibited conserved stress-induced expression, while others displayed species-, tissue-, or pathogen-specific patterns. Collectively, this study establishes an integrative evolutionary and stress-responsive framework for PME genes in cucurbits, providing mechanistic insights into cell wall plasticity and identifying candidate PME targets for improving multi-stress resilience in crop breeding.

bioinformatics↗

bioRxiv2025

Multilayered Transcriptomic Reprogramming and Spliceosomal Divergence Shape Bipolaris sorokiniana Pathogenicity

Bipolaris sorokiniana, the causative agent of spot blotch of wheat, significantly limits wheat productivity. Despite the pathogens widespread impact, the in planta molecular mechanisms underpinning its virulence remain poorly characterized. We performed a comprehensive RNA-sequencing analysis of B. sorokiniana during attack on spot-blotch-resistant and susceptible wheat genotypes, integrating differentially expressed genes (DEGs), alternative splicing (AS) events, and identification of long non-coding RNAs (lncRNAs). The pathogen exhibited extensive host-genotype-dependent transcriptomic reprogramming, with 128 pathogen genes upregulated in the susceptible host. These genes were associated with ribosome biogenesis, RNA processing, and primary metabolic functions, supporting aggressive colonization. In contrast, pathogen attack on the resistant genotype triggered the upregulation of 58 pathogen genes associated with stress-responsive pathways, including sphingolipid and ceramide metabolism. This suggests a shift toward defensive metabolic reprogramming in the resistant host that restricted its proliferation. Our investigation uncovered five classes of AS events and 14 differentially expressed lncRNAs, revealing substantial post-transcriptional complexity. Notably, a subunit of the H/ACA small nucleolar ribonucleoprotein (snoRNP) complex emerged as a rare "triple-hit" candidate simultaneously identified as a DEG, differentially alternatively spliced gene, and target of a differentially expressed lncRNA, highlighting its potential as a central regulatory node in host-responsive stress adaptation. This study reveals a multilayered regulatory landscape involving transcriptional plasticity, alternative splicing, and lncRNA-mediated control, enabling B. sorokiniana to fine-tune its infection strategy in response to host resistance. This work advances the understanding of fungal pathogenesis and identifies molecular vulnerabilities that could be exploited for targeted, host-specific disease control.

bioinformatics↗