Data from: Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing

BACKGROUND: Rise of temperatures and shortening of available water as result of predicted climate change will impose significant pressure on long-lived forest tree species. Discovering allelic variation present in drought related genes of two Austrian oak species can be the key to understand mechanisms of natural selection and provide forestry with key tools to cope with future challenges. RESULTS: In the present study we have used Roche 454 sequencing and developed a bioinformatic pipeline to process multiplexed tagged amplicons in order to identify single nucleotide polymorphisms and allelic sequences of ten candidate genes related to drought/osmotic stress from sessile oak (Quercus robur) and pedunculate oak (Q. petraea) individuals. Out of these, eight genes of 336 oak individuals growing in Austria have been detected with a total number of 158 polymorphic sites. Allele numbers ranged from ten to 52 with observed heterozygosity ranging from 0.115 to 0.640. All loci deviated from Hardy-Weinberg equilibrium and linkage disequilibrium was found among six combinations of loci. CONCLUSIONS: We have characterized 183 alleles of drought related genes from oak species and detected first evidences of natural selection. Beside the potential for marker development, we have created an expandable bioinformatic pipeline for the analysis of next generation sequencing data.背景：据预测，气候变化将引发气温升高与可利用水资源缩减，这将对长寿林木物种造成显著生存压力。针对奥地利境内两种橡树的干旱相关基因开展等位基因变异研究，或可为解析自然选择作用机制提供关键思路，同时为林业应对未来挑战提供核心技术工具。 结果：本研究采用罗氏454测序技术（Roche 454 sequencing），搭建了一套生物信息学分析流程以处理带标签的多重扩增子，旨在从奥地利境内的夏栎（Quercus robur）与无梗花栎（Q. petraea）个体中，筛选出10个与干旱/渗透胁迫相关的候选基因的单核苷酸多态性（single nucleotide polymorphism）位点及等位基因序列。最终在奥地利境内336株橡树个体中成功检测到其中8个基因，共计158个多态性位点。等位基因数介于10至52之间，观测杂合度范围为0.115至0.640。所有位点均偏离哈迪-温伯格平衡，且在6组位点组合间检测到连锁不平衡现象。 结论：本研究完成了橡树物种干旱相关基因的183个等位基因的特征解析，并首次检测到自然选择的相关证据。除可用于分子标记开发外，本研究还搭建了一套可扩展的生物信息学分析流程，用于下一代测序数据的分析。