Transcriptomic Profiling of Gossypium barbadense Under Fusarium oxysporum f. sp. vasinfectum Race 7 Infection via Bulk RNA-Seq and snRNA-Seq
4 affiliations
- 1College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China
- 2Institute of Forest Ecology and Landscaping, Xinjiang Academy of Forestry Sciences, Urumqi 830063, China
- 3Engineering Research Centre of Cotton, Ministry of Education, Urumqi 830052, China
- 4Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
Abstract
Cotton, as an economically important crop, suffers significant yield losses from infection by Fusarium oxysporum f. sp. vasinfectum race 7 (Fov7) infection. To elucidate the molecular mechanisms underlying host responses to Fov7 infection, we conducted a comprehensive transcriptional analysis of Gossypium barbadense using integrated bulk RNA sequencing (RNA-seq) and single-nucleus RNA sequencing (snRNA-seq) approaches. Our time-course study encompassed four critical infection stages (0, 2, 12, and 48 h post-inoculation) to characterize spatiotemporal transcriptomic dynamics. Bulk RNA-seq analysis revealed that the number of differentially expressed gene (DEG) numbers peaked at 2 h post-inoculation (hpi), identifying 9230 DEGs and demonstrating substantial transcriptional activation during early pathogen challenge. K-means clustering classified DEGs into six temporal expression patterns, with cluster C4 showing significant enrichment of defense-related pathways. Weighted gene co-expression network analysis (WGCNA) identified ten distinct co-expression modules, among which the turquoise module exhibited strong correlation with early infection responses. Integration of K-means clustering and WGCNA results pinpointed 1503 key defense-related genes. A single-nucleus atlas of cotton roots during Fov7 infection was constructed, comprising 32,773 nuclei, which revealed the cellular heterogeneity of cotton root tips. Functional enrichment analysis using these key genes emphasized the crucial roles of root cap and epidermal cells in pathogen perception and defense activation. Pseudotime trajectory mapping further delineated transcriptional dynamics in these cell populations during infection progression, demonstrating pathway activation in the root cap and epidermis at later infection stages. This multi-omics study establishes a valuable transcriptional resource for dissecting cotton’s resistance mechanisms against Fov7 and provides theoretical insights for developing disease-resistant cultivars through molecular breeding strategies.
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BibTeX
@article{liu2026transcriptomic,
title = {{Transcriptomic Profiling of Gossypium barbadense Under Fusarium oxysporum f. sp. vasinfectum Race 7 Infection via Bulk RNA-Seq and snRNA-Seq}},
author = {Baojun Liu and Gang Liu and Jianyu Bai and Yujia Zhang and Shu Wang and Aixing Gu and W. G. Dilantha Fernando},
journal = {Cells},
year = {2026},
month = oct,
doi = {10.3390/cells15211935},
url = {https://www.mdpi.com/2073-4409/15/21/1935},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Transcriptomic Profiling of Gossypium barbadense Under Fusarium oxysporum f. sp. vasinfectum Race 7 Infection via Bulk RNA-Seq and snRNA-Seq
AU - Baojun Liu
AU - Gang Liu
AU - Jianyu Bai
AU - Yujia Zhang
AU - Shu Wang
AU - Aixing Gu
AU - W. G. Dilantha Fernando
PY - 2026
DA - 2026/10/24
JO - Cells
DO - 10.3390/cells15211935
UR - https://www.mdpi.com/2073-4409/15/21/1935
AB - Cotton, as an economically important crop, suffers significant yield losses from infection by Fusarium oxysporum f. sp. vasinfectum race 7 (Fov7) infection. To elucidate the molecular mechanisms underlying host responses to Fov7 infection, we conducted a comprehensive transcriptional analysis of Gossypium barbadense using integrated bulk RNA sequencing (RNA-seq) and single-nucleus RNA sequencing (snRNA-seq) approaches. Our time-course study encompassed four critical infection stages (0, 2, 12, and 48 h post-inoculation) to characterize spatiotemporal transcriptomic dynamics. Bulk RNA-seq analysis revealed that the number of differentially expressed gene (DEG) numbers peaked at 2 h post-inoculation (hpi), identifying 9230 DEGs and demonstrating substantial transcriptional activation during early pathogen challenge. K-means clustering classified DEGs into six temporal expression patterns, with cluster C4 showing significant enrichment of defense-related pathways. Weighted gene co-expression network analysis (WGCNA) identified ten distinct co-expression modules, among which the turquoise module exhibited strong correlation with early infection responses. Integration of K-means clustering and WGCNA results pinpointed 1503 key defense-related genes. A single-nucleus atlas of cotton roots during Fov7 infection was constructed, comprising 32,773 nuclei, which revealed the cellular heterogeneity of cotton root tips. Functional enrichment analysis using these key genes emphasized the crucial roles of root cap and epidermal cells in pathogen perception and defense activation. Pseudotime trajectory mapping further delineated transcriptional dynamics in these cell populations during infection progression, demonstrating pathway activation in the root cap and epidermis at later infection stages. This multi-omics study establishes a valuable transcriptional resource for dissecting cotton’s resistance mechanisms against Fov7 and provides theoretical insights for developing disease-resistant cultivars through molecular breeding strategies.
SN - 2073-4409
ER -