Annotation of transcripts in darkred module.

Cryptomeria japonica is a coniferous species widely distributed throughout Japan and is therefore adapted to a variety of environments. To identify genes involved in its local adaptation, individuals of different origins growing in three common gardens located in the southern, central, and northern regions of Japan were subjected to transcriptome analysis. A transcriptome assembly guided by the whole-genome sequence of C. japonica yielded 77,212 transcripts derived from 56,203 genes. Based on single nucleotide polymorphisms (SNPs) detected in the transcriptome data, individuals were grouped into three genetic clusters. A total of 151 SNPs associated with population differentiation were detected using pcadapt. Of these, the allele frequencies of 40 SNPs showed associations with climatic variables, and the expression levels of genes containing 9 of these SNPs were also correlated with climatic variables. To further explore transcriptomic patterns underlying adaptation, weighted gene co-expression network analysis identified 25 gene modules. A comparison between representative expression patterns of each gene module and the 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 highly expressed in individuals from the Sea of Japan side (ura-sugi). These findings suggest that local adaptation in C. japonica involves not only responses to abiotic stress but also a significant contribution from genes involved in responses to biotic stress.

柳杉（Cryptomeria japonica）是一种广泛分布于日本全境的针叶树种，因此能够适应多种生境。为鉴定参与其本地适应的基因，研究人员对生长在日本南部、中部和北部3个同质种植园的不同起源个体开展了转录组分析。基于柳杉全基因组序列指导的转录组组装，共获得来自56203个基因的77212条转录本。基于转录组数据中检测到的单核苷酸多态性（single nucleotide polymorphisms, SNPs），研究人员将个体划分为3个遗传聚类群。借助pcadapt软件共检测到151个与种群分化相关的SNPs。其中，40个SNPs的等位基因频率与气候变量存在关联，且携带其中9个SNPs的基因的表达水平同样与气候变量呈显著相关。为进一步探究适应背后的转录组调控模式，研究人员采用加权基因共表达网络分析，共鉴定出25个基因模块。将每个基因模块的典型表达模式与SNPs预测的遗传分化进行对比后发现，在3个同质种植园中，有1个模块呈负相关，另有1个模块呈正相关。太平洋沿岸地区个体（omote-sugi）的防御响应基因表达量较高，而日本海沿岸地区个体（ura-sugi）的萜类代谢基因表达量则更为显著。上述研究结果表明，柳杉的本地适应不仅涉及对非生物胁迫的响应，同时也有参与生物胁迫响应的基因发挥重要作用。