A plea to DNA barcode type specimens: An example from<i>Micropholis</i>(Sapotaceae)

Sánchez‐C., Dayana; Richardson, James E.; Hart, Michelle; Serrano, Julieth; González, Mailyn; Cortés‐B, Rocío

doi:10.1002/tax.12652

Cited by 4 publications

(4 citation statements)

References 79 publications

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“…For example, selecting samples that have been checked by a taxonomic specialist in the group increases confidence in species determinations. In addition, with the relevant permissions, it is also possible to sequence type specimens to support a species name (Sánchez-C. et al, 2022). On the other hand, the DNA in herbaria and silica-dried samples is likely to have degraded due to the preservation techniques used and the passage of time, with many DNA fragments shorter than 100 bp (Weiß et al, 2016;Forrest et al, 2019).…”

Section: Sources Of Plant Samplesmentioning

confidence: 99%

Target capture and genome skimming for plant diversity studies

et al. 2023

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Recent technological advances in long‐read high‐throughput sequencing and assembly methods have facilitated the generation of annotated chromosome‐scale whole‐genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high‐molecular‐weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast‐freeze newly collected living samples to conserve high‐quality DNA can be complicated when plants are only found in remote areas. Therefore, short‐read reduced‐genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non‐model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best‐informed choice regarding reduced genome representation for evolutionary studies of non‐model plants in cases where whole‐genome sequencing remains impractical.

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Section: Sources Of Plant Samplesmentioning

confidence: 99%

Target capture and genome skimming for plant diversity studies

et al. 2023

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“…Preserved museum specimens can also be used to generate DNA barcodes [56]. It is significant that one recent study has encouraged a large-scale effort to sequence DNA barcodes from all types of specimens [57]. All of these DNA sequences add to the library of standard DNA barcode markers even if they do not carry the official GenBank DNA barcode designation.…”

Section: Building the Plant Dna Barcode Librarymentioning

confidence: 99%

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Gostel

Kress

2022

Diversity

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DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role.

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“…In some cases, type specimen may be the only credible remnant available for species identification. Hence, genetic resources from voucher specimens and even type specimens are vital for accurate identification, taxonomic designations, and conservation [55]. Although extracting DNA from museum specimens can be a major challenge and potentially be destructive [56][57][58], the growth of museomics, the study of DNA sequences obtained from museum specimens, combined with phenetic data collected from key specimens, will provide new taxonomic, evolutionary, and conservation insights.…”

Section: Integrative Evidence-based Taxonomy For Biodiversity Conserv...mentioning

confidence: 99%

Taxonomic Uncertainty and Its Conservation Implications in Management, a Case from Pyrus hopeiensis (Rosaceae)

Jun

2022

Diversity

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Improved taxonomies and phylogenies are essential for understanding the evolution of organisms, the development of conservation plans, and the allocation of funds and resources, especially for threatened species with uncertain identities. Pears are an economically and nutritionally important fruit, and wild pear species are highly valued and protected because of their utility for the development of cultivars. Pyrus hopeiensis is an endangered species endemic to North China, which is sympatric with and difficult to distinguish from the widely distributed and morphologically similar species P. ussuriensis. To clarify its taxonomic identity, principal coordinate analysis was performed using 14 quantitative and qualitative characters from P. hopeiensis, P. ussuriensis, and P. phaeocarpa, and phylogenomic analysis was performed based on whole-genome resequencing and whole plastome data. Pyrus hopeiensis was synonymized with P. ussuriensis based on morphological and phylogenetic evidence, as well as our long-term field studies. Pyrus hopeiensis is proposed to be excluded from the list of local key protected wild plants. Given that the holotype of P. ussuriensis was not designated, a lectotype was designated in this work. Integrative evidence-based taxonomic study including museomics is suggested for organisms with uncertain identities, which will contribute to biodiversity conservation.

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A plea to DNA barcode type specimens: An example fromMicropholis(Sapotaceae)

Cited by 4 publications

References 79 publications

Target capture and genome skimming for plant diversity studies

Target capture and genome skimming for plant diversity studies

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Taxonomic Uncertainty and Its Conservation Implications in Management, a Case from Pyrus hopeiensis (Rosaceae)

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