ArticlePlant methods2020
Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics.
Article in Plant methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Plant species identification by genome skimming across the vascular plant tree of life.The New phytologist · 2026Article
- Herbariomic approach solved identity crisis of the putatively extinct Armeria arcuata Welw. ex Boiss. & Reut. (Plumbaginaceae).Annals of botany · 2026Article
- Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.Molecular ecology resources · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Article
- Backbone phylogeny ofPlant diversity · 2025Article
- Exploring Structural Plastome Evolution in Asterales: Insights from Off-Target Hybrid Enrichment Data on the Small Single-Copy Region.Journal of molecular evolution · 2025Article
- From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification.Genes · 2024Review
- Article
- Skmer approach improves species discrimination in taxonomically problematic genusPlant diversity · 2024Article
- Exploring Taxonomic and Genetic Relationships in theInternational journal of molecular sciences · 2024Article
- Population genomics and morphological data bridge the centuries of cyanobacterial taxonomy along the continuum ofiScience · 2024Article
- Nuclear Magnetic Resonance Fingerprints and Mini DNA Markers for the Authentication of Cinnamon Species Ingredients Used in Food and Natural Health Products.Plants (Basel, Switzerland) · 2024Article
- LocoGSE, a sequence-based genome size estimator for plants.Frontiers in plant science · 2024Article
- Article
- Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships.BMC genomics · 2023Article
- Seed protein biotyping in Amaranthus species: a tool for rapid identification of weedy amaranths of concern.Plant methods · 2023Article
- New insights into the plastome evolution of Lauraceae using herbariomics.BMC plant biology · 2023Article
- Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years.Current genomics · 2023Review
- Intraspecific phylogeny and genomic resources development for an important medical plantFrontiers in plant science · 2023Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHerbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara.
resultsGenome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions
conclusionsWe showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.
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