Comparative Transcriptomics Reveals Divergent Expression Patterns Related to Carbon Metabolism, Transport, and Regulation in Juvenile Stems of Four Fagaceae Species

Background/Objectives: We compared juvenile whole-stem transcriptomes of Quercus glauca, Quercus acutissima, Quercus fabri, and Castanopsis sclerophylla to examine carbon metabolism and transport. Methods: Three seedlings per species were sampled in one session. RNA sequencing (RNA-seq) data were analyzed using differential-expression analysis, direction-specific Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, gene set enrichment analysis (GSEA), and leading-edge analysis. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed on aliquots from the same RNA extractions. Results: Reference-based analyses identified 8596–11,823 differentially expressed genes across six contrasts. GSEA detected 25 significant pathway-by-contrast associations across 13 pathways at a false discovery rate below 0.05. Q. glauca showed photosynthesis, starch turnover, and flavonoid pathway signals. Q. acutissima showed sugar-metabolism and ATP-binding cassette (ABC) transport signals, with XTH23 providing an annotation-based wall-remodeling candidate. Q. fabri showed enrichment of sulfur amino acid metabolism, nucleotide sugar metabolism, and mitogen-activated protein kinase signaling. C. sclerophylla showed ABC transport and galactose metabolism enrichment, with candidates annotated for raffinose synthesis and extracellular sucrose cleavage. Eleven of 12 candidates were present in at least one significant GSEA leading edge; XTH23 was selected using differential expression and annotation. Both assays identified the same species as having the highest expression for every candidate; eight genes also showed the same rank order across all four species. Conclusions: The sampled stems differed in the expression of genes associated with carbon metabolism, transport, and regulation. These whole-stem patterns provide candidates for tissue-resolved and physiological studies.