Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

Chua, Physilia; Leerhøi, Frederik; Langkjær, Emilia Marie Rolander; Noer, Christina Lehmkuhl; Richter, Stine Raith; Restrup, Marlene Elise Møller; Bruun, Hans Henrik; Hartvig, Ida; Coissac, Éric; Boessenkool, Sanne; Alsos, Inger Greve; Bohmann, Kristine

doi:10.1101/2021.08.11.456029

Cited by 2 publications

(1 citation statement)

References 84 publications

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“…Coissac et al (2016) suggested a workflow for building extended barcode reference libraries based on shotgun sequencing. Chua et al (2021) used genome skimming to generate an extended BRD for 184 plant species from Denmark. Alsos et al (2020) used genome skimming to build a reference database for the full chloroplast genome and the nrDNA cluster.…”

Section: Plant Dna Barcodes: Primers Markers and Databasesmentioning

confidence: 99%

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

et al. 2023

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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.

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Section: Plant Dna Barcodes: Primers Markers and Databasesmentioning

confidence: 99%

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

et al. 2023

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Data Release: DNA Barcodes of Plant Species Collected for the Global Genome Initiative for Gardens (GGI-Gardens) II

et al. 2022

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The Global Genome Initiative for Gardens (GGI-Gardens) is an international partnership of botanic gardens and arboreta that aims to preserve and understand the genomic diversity of plants on Earth. GGI-Gardens has organized a collection program focused on the living collections that partner institutions and supports the preservation of herbarium and genomic vouchers. Collections made through GGI-Gardens are deposited in recognized herbaria and Global Genome Biodiversity Network-partnered biorepositories worldwide, meaning that they are made available to the public. With support from its parent organization, the Global Genome Initiative (GGI), plant DNA barcode sequencing is performed using tissues collected through this partnership that represent taxa without barcode sequences in GenBank. This is the second data release published by GGI-Gardens and constitutes 2722 barcode sequences from 174 families and 702 genera of land plants. All DNA barcodes generated in this study are now available through the Barcode of Life Data Systems (BOLD) and GenBank.

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Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

Cited by 2 publications

References 84 publications

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

Toward freshwater plant diversity surveys with eDNA barcoding and metabarcoding

Data Release: DNA Barcodes of Plant Species Collected for the Global Genome Initiative for Gardens (GGI-Gardens) II

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