Project Details
Projekt
Making efficient use of herbarium specimens – Hybrids in Veronica as case example
Applicant
Professor Dr. Dirk Albach
Subject Area
Evolution and Systematics of Plants and Fungi
Term
since 2020
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 447018090
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.
DFG Programme
Priority Programmes
