DNA metabarcoding data unveils invisible pollination networks. J. Mar.

U.S.A. 108, 19641–19646.

All authors were involved in manuscript inception. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. Firstly, it is now common practice for herbaria to include material suitable for DNA extraction in their field collection protocols; leaf or other suitable tissue can now be routinely used for DNA extraction without compromising the integrity of voucher specimens (Gaudeul and Rouhan, 2013; Funk et al., 2017).

High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration.

Impact Factor 2.416 | CiteScore 3More on impact ›, Herbarium collection-based plant evolutionary genetics and genomics DNA barcoding in plants: taxonomy in a new perspective.

Plant Sci.

Metabarcoding, thereby, can be used to profile or survey the microbial community, and other communities, present in a sample without needing to cultivate or isolate. Received: 08 June 2018; Accepted: 21 August 2018; Published: 13 September 2018. Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci. Sci. Of all the taxonomic groups to which barcoding and metabarcoding methods are applied, identification of plants is the most common (Figure 1). DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. 2:306. doi: 10.1038/s41559-017-0413-2, Kraaijeveld, K., Weger, L. A., Ventayol García, M., Buermans, H., Frank, J., Hiemstra, P. S., et al. A variety of animals, predominantly insects, but also some birds, reptiles and mammals, provide pollination services for the majority of wild and cultivated plants (Potts et al., 2016; Hung et al., 2018).

Plant Sci.

Proc.

Distrib.

Divers. (2017). Resour. Individual OTUs are then compared against existing DNA databases in order to identify the organisms they represent. metabarcoding, spoilage investigations, and shelf life studies. DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (rbcL plus matK) for 490 Vascular Plant Species. To be truly universal, metabarcoding would require the inclusion of multiple loci, each optimized to capture species-level resolution in different taxa (e.g., CO1 for fauna, matK/rbcL for plants, ITS for fungi). Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis. 56, 175–193. doi: 10.1007/s10531-014-0672-z, Thomsen, P. F., and Willerslev, E. (2015).

The challenge lies in developing synergies between these offerings to ensure that data links remain dynamic and updates to taxonomy propagate throughout the system. Borrell, Y. J., Miralles, L., Do Huu, H., Mohammed-Geba, K., and Garcia-Vazquez, E. (2017). Minimizing polymerase biases in metabarcoding. What is the succession of microbes during fermentation? DNA barcoding and the renaissance of taxonomy. Collingwood: CSIRO Publishing. doi: 10.1111/2041-210X.12647, Krehenwinkel, H., Wolf, M., Lim, J. Y., Rominger, A. J., Simison, W. B., and Gillespie, R. G. (2017b). Rep. 7:12. doi: 10.1038/srep41909, Xu, S. Z., Li, Z. Y., and Jin, X. H. (2018).

This provides a basis for the development of a comprehensive barcoding reference database for Australian plants. Evol. (2018). doi: 10.1111/1755-0998.12288, Krehenwinkel, H., Kennedy, S., Pekár, S., Gillespie, R. G., and Johnston, S. (2017a).

Despite improvements in extraction and sequencing of DNA from herbarium specimens, there remain issues with potential sequence modification and sequencing errors that need to be understood and accounted for in downstream analyses (Staats et al., 2011; Weiß et al., 2016). A recent review by a leading collections institution botanist states; “Collections are a gold mine of both information and tissue samples and more advances are on the way” (Funk, 2018).

doi: 10.3732/ajb.1400398, Shepherd, K. A., Perkins, A., Collins, J., Byrne, M., and Thiele, K. R. (2013). In the years that followed Herbert et al. Li, D. Z., Gao, L. M., Li, H. T., Wang, H., Ge, X. J., et al. It is well sampled and expertly curated across the nation's herbaria, coordinated through the Council of Heads of Australasian Herbaria (CHAH). Metabarcoding is an identification (ID) method for organisms (e.g., microorganisms, plants, and animals) combining two technologies: DNA barcoding and HTS.

The applications for a robust and comprehensive plant barcoding system in Australia are diverse, and represent a range of potential benefits both economically and ecologically. Holzforschung 71, 939–949. doi: 10.12705/655.9, Heberling, J. M., and Isaac, B. L. (2017). Diet assessment based on rumen contents: a comparison between DNA metabarcoding and macroscopy.

Does GenBank provide a reliable DNA barcode reference to identify small alien oysters invading the Mediterranean Sea? Front. Plant Sci. Sci. (2014). Various methods have been proposed to control for these biases to better facilitate accurate quantification of relative abundance from metabarcoding data, including the utilization of degenerate primers (Krehenwinkel et al., 2017a,b), incorporation of gene copy number information (Kembel et al., 2012) and the inclusion of control species to generate relative correction factors (Thomas et al., 2016). doi: 10.3897/BDJ.5.e11625, Funk, V. A., Hoch, P. C., Prather, L. A., and Wagner, W. L. (2005). doi: 10.1073/pnas.0700466104, Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., et al. PLoS ONE 3:e2802. doi: 10.1111/nph.14470, Pečnikar, Ž.F., and Buzan, E. V. (2014).

Rep. 7:17668. doi: 10.1038/s41598-017-17333-x, Kress, W. J., and Erickson, D. L. (2007). Kimmerling, N., Zuqert, O., Amitai, G., Gurevich, T., Armoza-Zvuloni, R., Kolesnikov, I., et al. 106, 12794–12797.

A., and Green, J. L. (2012). Legal Med. Int. 18, 128–136. (2018). A commentary on systematics and the cybertaxonomic-automation paradigm. 15:66. doi: 10.1186/s12866-015-0351-6, Buglione, M., Maselli, V., Rippa, D., De Filippo, G., Trapanese, M., and Fulgione, D. (2018). Appl. 20 years since the introduction of DNA barcoding: from theory to application. doi: 10.1016/j.tplants.2012.12.006. Metabarcoding can be applied to the analysis of gut contents, enabling dietary analysis of animals. Similarly to barcoding, the options for genomic regions to be applied to metabarcoding will expand as sequencing capabilities expand (Porter and Hajibabaei, 2018).

Which microbes may serve as indicators for product quality, flavor, or texture? Effective plant barcoding and metabarcoding applications require the following with respect to reference databases: (1) Inclusion of multiple individuals from a broad suite of taxa to encompass a high proportion (if not all) of the possible species and to capture intraspecific diversity; (2) Accurate taxonomic identification of the included reference specimens; (3) Curation of reference specimens to retain as a resource for further study; (4) Availability of suitable material for destructive sampling for DNA extraction; (5) Extraction of DNA for sequencing and archiving; (6) Sequencing of a broad range of genomic regions according to standard protocols; (7) Data analysis according to standard protocols and meta-data sharing nomenclature; (8) Data archiving according to standard protocols; (9) Data fit for purpose, including ongoing data curation, and easily available for broad utility. Only 14% of species had data for all three of the core loci (matK, rbcL, ITS). (2018). Notes 7, 355–364.

A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing. Metabarcode data sets are more comprehensive, many times quicker to produce, and are less reliant on taxonomic expertise than traditional methods (e.g.

26, 2765–2790. doi: 10.1111/j.1471-8286.2007.01678.x, Richardson, R. T., Lin, C.-H., Quijia, J. O., Riusech, N. S., Goodell, K., and Johnson, R. M. (2015a). BMC Microbiol. U. K. 95, 111–122. doi: 10.1177/0959683615612563, Anderson, B. M., Barrett, M. D., Krauss, S. L., and Thiele, K. (2016). Evol. Search terms in quotes will enable a more specific search e.g. (2018). R. Soc. PN was supported partly by the Australian Government through the Australian Research Council Industrial Transformation Training Centre for Mine Site Restoration (project number ICI150100041). Cronobacter: An Emerging Pathogen Under the Microscope. Excel file containing data for the paper. Int. New taxonomy and old collections: integrating DNA barcoding into the collection curation process. DNA metabarcoding techniques enable us to evaluate dietary differences at a lower taxonomic level which can be followed up to ascertain why species are selecting specific species of plants (i.e., are animals targeting specific nutrients, water, etc.). Resour. Taxon 57, 1304–1316. 12, 396–402. doi: 10.1515/dna-2015-0021, Nevill, P. G., Wallace, M. J., Miller, J. T., and Krauss, S. L. (2013). These issues make historic collections preserved in this way more unsuitable for DNA extractions. Mol. Those DNA sequences are then analyzed to identify which organisms (animals, plants, bacteria, fungi, virus, etc.)

The application of metabarcoding methods to ancient sedimentary DNA can also help elucidate historical ecosystem dynamics (Thomsen and Willerslev, 2015; Parducci et al., 2017) and has been shown to perform better than pollen analysis (Alsos et al., 2016; Niemeyer et al., 2017) for species richness estimation.

DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia. doi: 10.1073/pnas.0905845106. A plea for modern botanical collections to include DNA-friendly material.

Genet. DNA metabarcoding is defined as the barcoding of DNA or eDNA (environmental DNA) that allows for simultaneous identification of many taxa within the same (environmental) sample, however often within the same organism group.

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