Biology subjects

Kadoo, N.

Publications and source records attributed to Kadoo, N..

2 recordsLinked to original sources

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↗