Next‐generation sampling: Pairing genomics with herbarium specimens provides species‐level signal in Solidago (Asteraceae)

Abstract

Premise of the study:The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 1970 and 2010.Methods:Reduced representation libraries were prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs, and resulting reads were processed with the nonreference Universal Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering was used to assess the correspondence between genetic groups and morphologically defined species.Results:Library construction and sequencing were successful in 93 of 95 samples. The UNEAK pipeline identified 8470 single-nucleotide polymorphisms, and a filtered data set was analyzed for each of three Solidago subsections. Although results varied, clustering identified genomic groups that often corresponded to currently recognized species or groups of closely related species.Discussion:These results suggest that genotyping by sequencing is broadly applicable to DNAs obtained from herbarium specimens. The data obtained and their biological signal suggest that pairing genomics with large-scale herbarium sampling is a promising strategy in species-rich plant groups.

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century

“…Multiplex sequencing protocols for RAD/GBS often depend on an accurate quantification of high-molecular-weight DNA (Elshire et al, 2011). However, this requirement may be waning, as recent studies have used RAD/GBS on herbarium specimens, which may have degraded DNA (Beck and Semple, 2015). Little information is currently available about how markers discovered with RAD/GBS are distributed across the genome, although studies in wheat and barley suggest that these markers are uniformly spaced (Poland et al, 2012).…”

Herbarium genomics: skimming and plastomics from archival specimens

“…On the other hand, much of the angiosperm plant species-level phylogenetics literature of the past two decades has been based on plastome intergenic spacer regions such as trnL-F or trnH-psbA (e.g. Morton and Clegg 1993;Bakker et al 1999;Kelchner 2002;Borsch et al 2003;Borsch and Herbarium DNA was used for finding previously unknown sister groups for important crops (Sebastian et al 2010;Chomicki and Renner 2015), or in SNP analysis in genotyping by sequencing of species in Solidago (Asteraceae) (Beck and Semple 2015). To study historical pathogens, Yoshida et al (2014Yoshida et al ( , 2015 determined the genotype of the Phytophthora infestans (Mont.)…”

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…Most paleogenomic studies to date have focused on large vertebrates that inhabit cold or temperate areas or the close relatives of crop plants that have abundant genomic information available (Allaby et al, 2015;JaenickeDespres et al, 2003), although genome-scale sequencing approaches of herbarium material are increasingly being applied (Bakker et al, 2015;Beck and Semple, 2015;Besnard et al, 2014;Staats et al, 2013;Zedane et al, 2015). The ability to sequence herbarium specimens, which may represent the only samples available for rare, endangered, or extinct taxa, provides great promise towards understanding important issues from biogeographic history to domestication, taxonomy, and conservation.…”