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

在过去的30年里，植物标本馆的标本有了新的用途，作为各种研究问题的DNA来源，这些研究问题从遗传学开始，但目前已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正在上升，这意味着有时对珍贵的标本，例如模式标本进行破坏性取样。为了避免不必要的和最终重复破坏的模式标本，无损方法需要探索和破坏性的方法需要优化。建立在信息和经验，在以前的项目标本基因组学在婆婆纳subg。Pseudolysimachium，我们首先探索使用近红外光谱非破坏性估计植物标本的倍性水平。第二，我们探讨了植物标本馆材料中基因组学的局限性。以前的研究表明，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，这阻碍了稳健的系统发育假设的产生。如果诱饵是基于密切相关的基因组设计的，那么Hyb-seq会受到数据缺失的影响较小，但如果诱饵来自更远的相关来源，则会变得越来越不可靠。在这里，我们探讨了多重鸟枪基因分型（基因组略读）的限制，大多在以前的研究中，但现在包括标本馆标本确认为重要的是了解亚属的巴尔干半岛的成员的分类。我们，进一步，调查的要求，有一个密切相关的参考基因组进行分析。我们以前在亚属的调查表明，可用的转录组和来自姐妹亚属的基因组太远相关，因此，从头组装是一个更好的适合的数据。这当然取决于与研究生物的遗传距离，因此，我们将对与我们的焦点小组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.