Transcriptome differentiation in Cryptomeria japonica trees with different origins growing in the north and south of Japan

Cryptomeria japonica is a coniferous species widely distributed throughout Japan and therefore adapted to various environments. To seek genes involved in the local adaptation of this species, individuals with different origins growing at three common gardens located in the south, central and north of Japan were subjected to transcriptome analysis. The transcriptome assembly, guided by whole-genome sequence of C. japonica, resulted in 77,212 transcripts from 56,203 genes. Individuals were clustered into three genetic groups based on single nucleotide polymorphisms (SNPs) detected in 12,389 genes among them. Weighted gene co-expression network analysis (WGCNA) identified 25 gene modules. Comparison of representative gene expression patterns for each co-expression gene module with genetic differentiation predicted by SNPs revealed that one module exhibited a negative correlation and another a positive correlation across all three common gardens. While defense response genes were highly expressed in individuals from the Pacific Ocean side of Japan (omote-sugi), terpenoid metabolism genes were more expressed in individuals originating from the Sea of Japan side (ura-sugi). These results suggest that local adaptation associated with the alteration of gene regulation occurred in biotic stress response genes in C. japonica.