ArticleApplications in plant sciences2015
Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae).
Article in Applications in plant sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 42 citations in OpenAlex.
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- Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation.Ecology and evolution · 2020Article
- A basic ddRADseq two-enzyme protocol performs well with herbarium and silica-dried tissues across four genera.Applications in plant sciences · 2020Article
- Utilizing field collected insects for next generation sequencing: Effects of sampling, storage, and DNA extraction methods.Ecology and evolution · 2019Article
- 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice.Rice (New York, N.Y.) · 2019Article
- Sequencing the Plastid Genome of Giant Ragweed (Frontiers in plant science · 2019Article
- Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing.Frontiers in plant science · 2018Article
- Population genetics and adaptation to climate along elevation gradients in invasive Solidago canadensis.PloS one · 2017Article
- The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century.Applications in plant sciences · 2016Article
- Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon.American journal of botany · 2016Article
- Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae).Applications in plant sciences · 2015Article
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2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premise of the studyThe 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.
methodsReduced 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.
resultsLibrary 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.
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