Categorisation of lowly expressed cassava (Manihot esculenta)  genes activated by mealybug (Phenacoccus manihoti) infestation

Dinh Thi Hong Nhung; Le Do Hoai Thu; Nguyen Quoc Trung; Dong Huy Gioi; Duong Thanh Thuy; Nguyen Thi Hoai; Pham Truong Giang; Do Thi Lan Huong; Chu Duc Ha

doi:10.55250/Jo.vnuf.11.1.2026.011-020

Authors

Dinh Thi Hong Nhung University of Engineering and Technology, Vietnam National University Hanoi
Le Do Hoai Thu Hanoi Pedagogical University 2
Nguyen Quoc Trung Vietnam National University of Agriculture
Dong Huy Gioi Vietnam National University of Agriculture
Duong Thanh Thuy University of Agriculture and Forestry, Hue University
Nguyen Thi Hoai University of Agriculture and Forestry, Hue University
Pham Truong Giang Institute of Scientific Research and Application, Hanoi Pedagogical University 2
Do Thi Lan Huong Hanoi Pedagogical University 2
Chu Duc Ha University of Engineering and Technology, Vietnam National University Hanoi

DOI:

https://doi.org/10.55250/Jo.vnuf.11.1.2026.011-020

Keywords:

Cassava, differentially expressed gene, lowly expressed gene, mealybug, RNA-Seq

Abstract

Cassava (Manihot esculenta) plays a crucial role in food security and industrial use in tropical and subtropical regions. However, its productivity is severely affected by Phenacoccus manihoti (mealybug) infestation. While several studies have examined cassava's responses to abiotic stress, the molecular mechanisms driving cassava’s defence against mealybugs remain poorly understood. This study aimed to uncover the transcriptional dynamics of cassava leaves in the early stages of P. manihoti infestation by reanalysing public RNA-Seq datasets. The authors focused on genes that are lowly expressed under normal conditions, hypothesising that they may play inducible roles in stress responses. Our analysis revealed 546 such genes that became differentially expressed one day post-inoculation, including 263 up-regulated and 283 down-regulated genes. Functional enrichment indicated significant involvement in RNA biosynthesis and transcriptional regulation, phytohormone signaling (notably auxin-related pathways), lipid metabolism (especially glycerolipid biosynthesis), and secondary metabolism (such as phenolic compound production). Key transcription factors (e.g., WRKY, ERF, and MYB) and signaling modules (e.g., MAPK cascades) were also activated, pointing to a rapid reprogramming of the cassava transcriptome to mount an effective defence. Additionally, genes related to redox regulation, cell wall modification, and solute transport were enriched, suggesting a coordinated physiological response. This study provides new insights into the early inducible gene networks that contribute to cassava's defence against mealybug attack. These findings highlight novel genetic targets that can inform future molecular breeding and genome-editing strategies to enhance cassava’s resilience against mealybug infestation.

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