Shumskaya Maria, Mironov Kirill S, Ballesteros Jesús A, Safonov Igor, Halling Roy E
Department of Biology, CSMT Kean University Union New Jersey USA.
Department of Molecular Biosystems K.A. Timiryazev Institute of Plant Physiology Moscow Russian Federation.
Ecol Evol. 2023 Aug 10;13(8):e10389. doi: 10.1002/ece3.10389. eCollection 2023 Aug.
Molecular characterization of type specimens is a powerful tool used in clarifying species identity/circumscription, as well as establishing the taxonomic and phylogenetic status of organisms in question. However, DNA sequencing of aged herbarium collections can be a challenge due to the quantity and quality of DNA still present in the specimens. Herein, we report a custom DNA isolation protocol suitable for processing minute quantities of old specimen tissue and its utilization via high-throughput sequencing technologies to obtain, for the first time, the genome assembly of the 134-year-old holotype of Peck, a North American fleshy pored mushroom of taxonomic and historical significance. A side-by-side evaluation of our DNA isolation method with that of a commercial "kit" by Qiagen is also presented. By relying on the type material, we have established the genetic identity of , as well as providing preliminary phylogenetic evidence for its generic affinities in within Boletaceae. The reference genome of the holotype provides a resource for future comparative genomic studies, taxonomic revisions in Boletaceae, and other evolutionary studies of fungi.
模式标本的分子特征分析是用于明确物种身份/界定范围以及确定相关生物的分类和系统发育地位的有力工具。然而,由于标本中仍存在的DNA的数量和质量,对陈旧标本馆收藏进行DNA测序可能是一项挑战。在此,我们报告了一种适用于处理微量陈旧标本组织的定制DNA分离方案,以及通过高通量测序技术对其进行利用,从而首次获得了具有分类学和历史意义的北美肉质多孔蘑菇佩克(Peck)134年历史的全模式标本的基因组组装。我们还将我们的DNA分离方法与Qiagen的商业“试剂盒”方法进行了并行评估。通过依赖模式材料,我们确定了佩克的遗传身份,并为其在牛肝菌科内的属亲缘关系提供了初步的系统发育证据。全模式标本的参考基因组为未来的比较基因组研究、牛肝菌科的分类修订以及真菌的其他进化研究提供了资源。