Unveiling Key Genes and Unique Transcription Factors Involved in Secondary Cell Wall Formation in Pinus taeda

<i>Pinus taeda</i> is a key timber species, and extensive research has been conducted on its wood formation. However, a comprehensive investigation into the biosynthetic pathways of lignin, cellulose, and hemicellulose in <i>P. taeda</i> is lacking, resulting in an incomplete understanding of secondary cell wall (SCW) formation in this species. In this study, we systematically analyzed transcriptomic data from previously published sources and constructed detailed pathways for lignin, cellulose, and hemicellulose biosynthesis. We identified 188 lignin-related genes and 78 genes associated with cellulose and hemicellulose biosynthesis. An RT-qPCR highlighted 15 key lignin biosynthesis genes and 13 crucial genes for cellulose and hemicellulose biosynthesis. A STEM analysis showed that most essential enzyme-coding genes clustered into Profile 14, suggesting their significant role in SCW formation. Additionally, we identified seven NAC and six MYB transcription factors (TFs) from atypical evolutionary clades, with distinct expression patterns from those of the previously characterized <i>NAC</i> and <i>MYB</i> genes, indicating potentially unique functions in SCW formation. This research provides the first comprehensive overview of lignin, cellulose, and hemicellulose biosynthetic genes in <i>P. taeda</i> and underscores the importance of non-canonical NAC and MYB TFs, laying a genetic foundation for future studies on SCW regulatory mechanisms.