Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight, a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two D. septosporum isolates and analyzed the differentially expressed genes (DEGs), differential exon usage, and coexpressed gene modules using RNA-sequencing data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one D. septosporum isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene module–identified genes to the reference plant-pathogen interaction pathway deposited in the Kyoto Encyclopedia of Genes and Genomes database. These genes are present in PAMP-triggered and effector-triggered immunity pathways. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to D. septosporum effectors. Taken together, our results show that gene expression response to D. septosporum infection in lodgepole pine varies both among tree genotypes and pathogen strains and involves both known candidate genes and a number of genes with previously unknown functions.

Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

在生物和非生物条件下，许多针叶树的分布范围很广，但是对生物压力响应的基础比对非生物压力响应的关注要少得多。在这项研究中，我们调查了寄主松（Pinus contorta）对真菌病原体Dothistroma septosporum的攻击的基因表达反应，该病原引起Dothistroma针枯萎病，该疾病已导致不列颠哥伦比亚省西北部与气候有关的严重暴发。我们用两个D. septosporum接种了耐性和易感性的松树使用RNA测序数据分离并分析差异表达基因（DEG），差异外显子用法和共表达的基因模块。我们发现在接种一种D. septosporum的耐受性寄主松树样品中有快速而强大的转录组反应分离株，并且在接种另一种分离株的易感样品中有较晚和较弱的响应。我们将DEG或基因模块识别的基因中的43个映射到保存在《京都基因与基因组百科全书》数据库中的参考植物-病原体相互作用途径。这些基因存在于PAMP触发和效应子触发的免疫途径中。包含途径和基因模块的基因具有很强的选择性约束特征，而耐受性样品中高表达的基因似乎已受到选择的青睐，以抵抗病原体。我们确定了可能对D. septosporum效应子有反应的候选抗性基因。两者合计，我们的结果表明基因表达对D. septosporum的反应 在黑松中的感染在树型和病原体菌株之间都不同，并且涉及已知的候选基因和许多以前未知功能的基因。

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