Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata

Area of Science:

• Wood Science
• Plant Molecular Biology
• Genomics

Background:

• Compression wood (CW) in gymnosperms poses challenges for the wood industry due to altered properties.
• Chinese fir (Cunninghamia lanceolata) is a significant timber species in China.
• Transcriptome profiling of CW formation in gymnosperms remains largely unexplored.

Purpose of the Study:

• To characterize the morphological and cytological differences between compression wood (CW) and normal wood (NW) in Chinese fir.
• To perform a global transcriptome profiling of coding and long non-coding RNAs in response to compression stress.
• To identify candidate genes and regulatory pathways involved in CW formation.

Main Methods:

• PacBio long-read SMRT sequencing (Iso-Seq) and Illumina short-read RNA-Seq were employed.
• Transcriptome analysis was conducted on stem-differentiating xylem (SDX) under compression stress at multiple time points.
• Differential gene expression analysis and correlation analysis between coding and non-coding RNAs were performed.

Main Results:

• Distinct CW morphology with high lignin content and altered tracheid cells was observed.
• A comprehensive full-length transcriptome reference was assembled, revealing differential expression of genes in lignin and cellulose synthesis pathways.
• 11 secondary growth-related transcription factors and 6,533 coding genes along with 372 long non-coding RNAs (lncRNAs) showed differential expression.

Conclusions:

• This study provides the first comprehensive cytology and full-length transcriptome profiling of wood under compression stress in gymnosperm Chinese fir.
• Candidate genes, including coding and lncRNAs, involved in cell wall biogenesis and xyloglucan metabolism were identified.
• The findings offer a theoretical foundation for understanding the formation mechanism of CW in gymnosperms.