RNA-seq-based SNP discovery and functional characterization reveal genetic variation and evolutionary insights in Cinnamomum species

Abstract&nbsp; <br> &nbsp; <br> Genetic differences are essential for the adaptability,&nbsp; resilience, and evolutionary success of plant species.&nbsp; Cinnamomum, a genus of commercial and therapeutic&nbsp; significance, remains little studied at the genomic level. In&nbsp; this study, we conducted a comprehensive RNA-Seq-based&nbsp; single nucleotide polymorphism (SNP) analysis on six&nbsp; transcriptome samples from C. camphora and C. verum,&nbsp; aligned with the C. kanehirae reference genome. We&nbsp; identified a total of 184,532 high-confidence SNPs,&nbsp; comprising 410,247 missense SNPs and 397,053&nbsp; synonymous SNPs, yielding a missense-to-synonymous&nbsp; ratio of 1.03. Chromosome-wide analysis revealed that&nbsp; chromosome QPKB01000001.1 contained the highest SNP&nbsp; count (12,458 SNPs), whereas QPKB01000005.1 exhibited&nbsp; the strongest population differentiation, with a mean FST&nbsp; value of 0.342. A strong positive correlation (r = 0.79, p &lt;&nbsp; 0.001) was observed between SNP density and&nbsp; chromosomal length. Functional enrichment analysis&nbsp; demonstrated that SNP-associated genes were significantly&nbsp; enriched (FDR &lt; 0.05) in metabolic processes, cellular&nbsp; architecture, and regulatory pathways. KEGG annotation&nbsp; linked SNPs to significant metabolic pathways, including&nbsp; purine metabolism, phenylpropanoid biosynthesis (- log10(p) &gt; 5), and lignin biosynthesis. Analysis of linkage&nbsp; disequilibrium (LD) decay showed that the mean r² value&nbsp; dropped below 0.2 within approximately 50 kilobases,&nbsp; <br> indicating high recombination rates and low genome-wide&nbsp; LD. The allele frequency spectrum revealed a&nbsp; predominance of low-frequency variants (MAF &lt; 0.1),&nbsp; constituting over 60% of all SNPs, which suggests the&nbsp; influence of genetic drift and recent population expansion.&nbsp; Notably, over 20 genes exhibited an accumulation of more&nbsp; than 50 missense SNPs, highlighting potential targets of&nbsp; evolutionary selection. These results clarify the molecular&nbsp; and evolutionary dynamics of Cinnamomum species and&nbsp; provide a robust basis for additional research into plant&nbsp; adaptation, genetic conservation, and trait-based selection&nbsp; in non-model plant genomes.