European black pine (Pinus nigra J.F.Arnold) is an ecologically and economically important conifer growing across southern Europe and the Mediterranean Basin in a variety of habitats. Its morphological and ecological variabilities as well as geographic origin are the basis for subspecies level taxonomic identification and forestry practice recommendations. Yet, no true consensus exists and genomic resources are lacking for resolving the taxonomy of P. nigra and assessing its adaptive potential. To provide genetic tools for further research, we generated novel genomic resources using six de novo transcriptomic assemblies representing major biogeographic regions where the species is growing naturally. Using two closely related species, Pinus sylvestris and Pinus halepensis, as outgroups, we identified a set of 2200 nuclear, putatively orthologous, single-copy genes. In addition, we identified a set of 405,624 polymorphic SNPs for P. nigra. Based on these resources, we were able to confirm the division of P. nigra into two wide geographical population groups and to provide new insights into evolutionary dynamics of the species.

欧洲黑松（Pinus nigra JFArnold）是一种在生态和经济上很重要的针叶树，生长在欧洲南部和地中海盆地的各种生境中。其形态和生态变异性以及地理起源是亚种级分类学鉴定和林业实践建议的基础。但是，目前尚无真正的共识，而且缺乏解决黑皮病分类学和评估其适应潜力的基因组资源。为了提供进一步研究的遗传工具，我们使用了六个de novo转录组来代表物种自然生长的主要生物地理区域，从而产生了新颖的基因组资源。使用两个密切相关的物种，樟子松和哈尔滨松（Pinus halepensis）作为外群，我们鉴定了一组2200个核推定直系同源单拷贝基因。此外，我们确定了一组405,624个黑质多态性SNP 。基于这些资源，我们能够确定黑黑点球菌分为两个广泛的地理种群群，并提供了对该物种进化动力学的新见解。