Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo, Mexico

Hernández-León, Sergio; Little, Damon P.; Acevedo-Sandoval, Otilio A.; Gernandt, David S.; Rodríguez-Laguna, Rodrigo; Saucedo-García, Mariana; Arce-Cervantes, Oscar; Razo-Zárate, Ramón; Espitia-López, Josefa

doi:10.1080/14772000.2018.1546240

Cited by 4 publications

(1 citation statement)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Forest monitoring plots, such as the Smithsonian's Forest Global Earth Observatories (ForestGEO) and the National Science Foundation's Long Term Ecological Research (LTER) sites, are rich resources because they have well-verified identifications, vouchered collections, and individually tagged trees that can be revisited by botanists if necessary [43][44][45][46]. Even if no specific monitoring plots have been established, many studies have generated DNA barcode libraries for specific habitats [47], plant communities [48], or regional taxa [49][50][51] and are thereby expanding the global plant genetic library. Individual taxonomists are also generating DNA barcodes for specific groups of plants as either standard markers (e.g., [52][53][54][55]) or as an offshoot of their basic molecular phylogenetic investigations aimed at understanding evolutionary relationships.…”

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

View full text Add to dashboard Cite

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.

show abstract

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

View full text Add to dashboard Cite

show abstract

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

et al. 2023

View full text Add to dashboard Cite

Providing reliable, cost‐effective data on species distribution is critical to ensuring biodiversity conservation. However, many species may go unrecorded by conventional surveys, especially in aquatic environments. Environmental DNA (eDNA) barcoding and metabarcoding are alternative approaches that could complete biodiversity estimates based on species observations. While eDNA surveys are being standardized for some animal groups (e.g., fish and amphibians), research on eDNA approaches for freshwater plant communities is just starting to bear fruit. Here, we synthesized the 22 studies that used eDNA barcoding and metabarcoding to survey plant biodiversity in freshwater systems. We present evidence that contemporary aquatic plants (macrophytes) and terrestrial plants can be detected in water and surficial sediment eDNA from lakes and rivers. The phenology (e.g., senescence) of the target taxa strongly influences species detection. The main application of eDNA barcoding targets the monitoring of invasive macrophytes, and barcoding assays are available for 14 taxa. The metabarcoding approach shows a range of applications: the detection of rare macrophytes, catchment‐scale floristic inventories, and sediment fingerprinting. Barcodes on the plastid genome (cpDNA) are preferred for both approaches: matK and trnH‐psbA for barcoding, trnL, and rbcL for metabarcoding. The intergenic transcribed spacer 1 (ITS1) from the nuclear ribosomal DNA (nrDNA) was used for designing eDNA barcoding assays on five invasive macrophytes. In contrast, only three metabarcoding studies used the ITS1 or IST2 with newly designed primers. However, metabarcoding applications should routinely use a multi‐locus approach, combining cpDNA and nrDNA barcodes. Barcode combinations and existing primers need further testing on eDNA samples. We recommend using local barcode reference databases (BRDs), ideally self‐made, to circumvent taxonomic gaps and heterogeneous sequences in public BRDs. Finally, new technologies and developments like droplet digital PCR and hybridisation capture offer new perspectives for eDNA‐based biodiversity monitoring approaches.

show abstract

Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers

et al. 2020

View full text Add to dashboard Cite

Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo, Mexico

Cited by 4 publications

References 66 publications

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

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

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

Re-evaluation of the phylogenetic relationships and species delimitation of two closely related families (Lamiaceae and Verbenaceae) using two DNA barcode markers

Contact Info

Product

Resources

About