Making efficient use of herbarium specimens – Hybrids in Veronica as case example

在过去的30年里，植物标本室标本有了新的用途，作为各种研究问题的DNA来源，从系统遗传学开始，现在扩展到基因组学和功能遗传学。因此，为DNA提取提供材料的压力越来越大，这意味着有时会对珍贵标本（例如模式标本）进行破坏性取样。为了避免对模式试样进行不必要的、最终的重复破坏，需要探索无损方法，并对破坏性方法进行优化。在Veronica subg以前的植物标本室基因组学项目的信息和经验的基础上。本文首先探讨了利用近红外光谱对植物标本馆标本倍性水平的无损估计。其次，我们探讨了基因组学在植物标本馆材料中的局限性。先前的研究表明，GBS（或相关的RAD-seq方法）和基于微流控PCR的扩增子测序存在大量缺失数据，无法产生可靠的系统发育假设。如果诱饵是基于密切相关的基因组设计的，Hyb-seq受数据缺失的影响较小，但如果诱饵来自更遥远的来源，则会变得越来越不可靠。在这里，我们探讨了多重猎枪基因分型（基因组略读）的局限性，这些样本主要是在以前的研究中调查过的，但现在包括了被认为对了解巴尔干亚属成员的分类学很重要的植物标本馆标本。我们进一步研究了对密切相关的参考基因组进行分析的要求。我们之前在亚属中的研究表明，可用的转录组和来自姐妹亚属的基因组关系太遥远，因此，从头组装更适合数据。这当然取决于与研究生物体的遗传距离，因此，我们将对与我们的焦点群体相关的三个基因组进行测序。

The last 30 years has seen a new use of herbarium specimens, as source of DNA for a variety of research questions starting with phylogenetics but currently expanding to genomics and functional genetics. Consequently, pressure to provide material for DNA extraction is rising, which means destructive sampling of sometimes precious specimens, e.g. type specimens. To avoid unnecessary and eventually repeated destruction of type specimens, nondestructive methods need to be explored and destructive methods need to be optimized. Building on the information and experience in previous projects on herbarium genomics in Veronica subg. Pseudolysimachium, we first explore the use of Near Infrared-spectroscopy to non-destructively estimate ploidy levels of herbarium specimens. Second, we explore the limits of genomics in herbarium material. Previous investigations have shown that GBS (or related RAD-seq methods) and amplicon sequencing based on microfluidic PCR suffer from large amounts of missing data preventing the generation of robust phylogenetic hypotheses. Hyb-seq suffers less from missing data if baits are designed based on closely related genomes but become increasingly unreliable if baits are from more distantly related sources. Here, we explore the limits of multiplex shotgun genotyping (genome skimming) on samples mostly investigated in previous studies but now including herbarium specimens recognized as important to understand the taxonomy of the Balkan members of the subgenus. We, further, investigate the requirement to have a closely related reference genome for analyses. Our previous investigations in the subgenus demonstrated that available transcriptomes and a genome from the sister subgenus are too distantly related and, thus, de novo-assemblies are a better fit for the data. This certainly depends on the genetic distance from the study organisms and we will, therefore, sequence three genomes variably related to our focus group.