Gene expression differences between western redcedar seedlings resistant and susceptible to cedar leaf blight

Western redcedar (T. plicata) is an important Cupressaceae both at economic and cultural levels in the Pacific Northwest of North America. In adult trees, the species produces one of the most weathering-resistant heartwoods among conifers, making it one of the preferred species for outdoor applications. However, young T. plicata plants are susceptible to infection with cedar leaf blight (D. thujina), an important foliar pathogen that can be devastating in nurseries and small-spaced plantations. Despite that, variability in the resistance against D. thujina in T. plicata has been documented, and such a variability can be used to breed T. plicata for resistance against the pathogen. This investigation aimed to discern the phenotypic and gene expression differences between resistant and susceptible T. plicata seedlings to shed light on the potential constitutive resistance mechanisms against cedar leaf blight in western redcedar. The study consisted of two parts. First, the histological di..., This dataset includes transcriptomic and gene expression data from an investigation on the impact of Didymascella thujina (cedar leaf blight) on Thuja plicata (western redcedar). The datasets included in this submission were collected and produced as follows below. The information shown here was extracted from the manuscript:
RNA extraction, mRNA enrichment, library production and sequencing
RNA extraction from foliage of three CLB+ and three CLB- seedlings was done using a modified version of the protocol of Rajakani et al. (2013) [...]. mRNA enrichment was done using protocol C of the Thermo Scientific™ MagJET mRNA Enrichment Kit (Life Technologies Inc., Burlington ON, Canada). Libraries were made using the NEB Next® Ultra™ RNA Library Prep Kit for Illumina® v. 1.2. (New England BioLabs® Inc., Ipswich MA, USA). DNA was purified as required using the Thermo Scientific GeneJET NGS Cleanup Kit (Life Technologies Inc.), and size selection (∼450 bp fragment size) was completed with the The..., , # Gene expression differences between Western Redcedar seedlings resistant and susceptible to Cedar Leaf Blight

The sets deposited here include 1) the transcriptomic assembly, and 2) the differential expression data produced from an investigation that aimed to detect constitutive differences between *Thuja plicata* (western redcedar) seedlings that were susceptible or resistant to *Didymascella thujina* (cedar leaf blight, CLB). The study also included histological and foliar chemical composition components, but those data are part of the manuscript itself.

The assembled transcriptome can be considered a metagenome as sequences annotated as belonging to organisms other than *T. plicata* or *D. thujina* were not removed unless they did not meet the minimum nucleotide length. That approach was taken in case that organisms other than *T. plicata* could account for resistance against *D. thujina* in this pathosystem (e.g. due to endosymbionts), which could have been overlooked if just a...

西部红柏（Thuja plicata，缩写T. plicata）是北美太平洋西北地区在经济与文化层面均具有重要价值的柏科（Cupressaceae）树种。成年个体的心材是针叶树中耐候性最优的心材之一，因此成为户外应用的首选树种之一。然而，幼年北美乔柏易受柏树叶枯病（cedar leaf blight，缩写CLB）病原菌——多毛壳孢叶枯病菌（Didymascella thujina，缩写D. thujina）——侵染，该叶部病原菌可对苗圃及密植人工林造成毁灭性危害。尽管如此，已有研究证实北美乔柏对D. thujina的抗性存在遗传变异，这一特性可用于培育抗该病原菌的北美乔柏品种。本研究旨在明确抗感北美乔柏幼苗间的表型与基因表达差异，以揭示西部红柏抗柏树叶枯病的潜在组成型抗性机制。本研究分为两部分：首先为组织学分析……本数据集包含一项针对多毛壳孢叶枯病菌（Didymascella thujina，即柏树叶枯病，CLB）对北美乔柏（Thuja plicata，西部红柏）影响的转录组学与基因表达研究数据。本次提交的数据集采集与制备流程如下，以下信息均提取自研究手稿：

采用改良自Rajakani等人（2013）的实验方案，从3株感病（CLB+）与3株抗病（CLB-）幼苗的叶片中提取RNA[……]。mRNA富集步骤使用赛默飞世尔科技旗下Thermo Scientific™ MagJET mRNA Enrichment Kit（加拿大安大略省伯灵顿市生命技术公司）的C方案。文库构建采用适配Illumina®平台的NEBNext® Ultra™ RNA Library Prep Kit for Illumina® v.1.2（美国马萨诸塞州伊普斯维奇市新英格兰生物实验室公司）。按照要求使用Thermo Scientific GeneJET NGS Cleanup Kit（生命技术公司）对DNA进行纯化，并完成约450bp片段大小的筛选……

# 抗柏树叶枯病的北美乔柏幼苗的基因表达差异

本次提交的数据集包含1）转录组组装结果，以及2）针对抗感柏树叶枯病的北美乔柏幼苗组成型表达差异分析得到的差异表达基因数据。本研究同时包含组织学与叶片化学成分分析数据，但相关内容已纳入研究手稿正文。

本次组装的转录组可被视为宏基因组，因为所有注释为非北美乔柏或非多毛壳孢叶枯病菌的序列，只要未达到最低核苷酸长度阈值，均未被移除。采用该策略的原因在于，本寄主-病原互作系统中，非北美乔柏的生物（例如内生共生菌）可能参与了对多毛壳孢叶枯病菌的抗性，若仅采用常规的宿主序列过滤方式，则可能遗漏此类关键因素……