Pinus taeda 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 P. taeda 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 NAC and MYB genes, indicating potentially unique functions in SCW formation. This research provides the first comprehensive overview of lignin, cellulose, and hemicellulose biosynthetic genes in P. taeda and underscores the importance of non-canonical NAC and MYB TFs, laying a genetic foundation for future studies on SCW regulatory mechanisms.

Proserpinaca palustris, a representative heterophyllous plant, represents an emerging model for studying morphological plasticity and adaptive evolution in amphibious environments. However, the absence of a high-quality reference genome has hindered molecular investigations into its heterophylly regulation mechanisms. Here, we present the first chromosome-level genome assembly of P. palustris. The final assembly spans 385.32 Mb, anchored onto seven pseudochromosomes (1n = 7), and encodes 22,756 predicted protein-coding genes. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment demonstrated high completeness, with scores of 95.61% for the genome assembly and 96.43% for the gene set. Comparative genomic analyses revealed that P. palustris underwent only the ancient γ whole-genome triplication (γ-WGT) event, with no subsequent whole-genome duplication (WGD). Nevertheless, the genome has experienced extensive re-diploidization, likely facilitated by structural rearrangements. Transcriptomic profiling identified three KNOTTED1-like homeobox (KNOX) genes (i.e., PPA02C1640, PPA03C1159, and PPA01C1293) that were significantly differentially expressed between submerged and terrestrial leaves in P. palustris, suggesting their potential role in regulating heterophylly. This study provides the first high-quality genomic resource for the genus Proserpinaca (Haloragaceae) and identifies key KNOX genes implicated in heterophylly regulation in P. palustris.