Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton.

ABSTRACT:

Background

Cold stress significantly challenges cotton growth and productivity, yet the genetic and molecular mechanisms underlying cold tolerance remain poorly understood.

Results

We employed RNA-seq and iterative weighted gene co-expression network analysis (WGCNA) to investigate gene and transposable element (TE) expression changes at six cold stress time points (0 h, 2 h, 4 h, 6 h, 12 h, 24 h). Thousands of differentially expressed genes (DEGs) were identified, exhibiting time-specific patterns that highlight a phase-dependent transcriptional response. While the A and D subgenomes contributed comparably to DEG numbers, numerous homeologous gene pairs showed differential expression, indicating regulatory divergence. Iterative WGCNA uncovered 125 gene co-expression modules

SUBMITTER: Dai Y 

PROVIDER: S-EPMC11900653 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature