{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T16:59:09Z","timestamp":1790787549451,"version":"4.1.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,2,4]],"date-time":"2020-02-04T00:00:00Z","timestamp":1580774400000},"content-version":"vor","delay-in-days":34,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Finanziamenti di Ateneo per progetti di Ricerca scientifica","award":["FRA2016"],"award-info":[{"award-number":["FRA2016"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>DNA metabarcoding combines DNA barcoding with high-throughput sequencing to identify different taxa within environmental communities. The ITS has already been proposed and widely used as universal barcode marker for plants, but a comprehensive, updated and accurate reference dataset of plant ITS sequences has not been available so far. Here, we constructed reference datasets of Viridiplantae ITS1, ITS2 and entire ITS sequences including both Chlorophyta and Streptophyta. The sequences were retrieved from NCBI, and the ITS region was extracted. The sequences underwent identity check to remove misidentified records and were clustered at 99% identity to reduce redundancy and computational effort. For this step, we developed a script called \u2018better clustering for QIIME\u2019 (bc4q) to ensure that the representative sequences are chosen according to the composition of the cluster at a different taxonomic level. The three datasets obtained with the bc4q script are PLANiTS1 (100\u2009224 sequences), PLANiTS2 (96\u2009771 sequences) and PLANiTS (97\u2009550 sequences), and all are pre-formatted for QIIME, being this the most used bioinformatic pipeline for metabarcoding analysis. Being curated and updated reference databases, PLANiTS1, PLANiTS2 and PLANiTS are proposed as a reliable, pivotal first step for a general standardization of plant DNA metabarcoding studies. The bc4q script is presented as a new tool useful in each research dealing with sequences clustering.<\/jats:p>\n                  <jats:p>Database URL: https:\/\/github.com\/apallavicini\/bc4q; https:\/\/github.com\/apallavicini\/PLANiTS.<\/jats:p>","DOI":"10.1093\/database\/baz155","type":"journal-article","created":{"date-parts":[[2020,1,8]],"date-time":"2020-01-08T23:18:36Z","timestamp":1578525516000},"source":"Crossref","is-referenced-by-count":131,"title":["PLANiTS: a curated sequence reference dataset for plant ITS DNA metabarcoding"],"prefix":"10.1093","volume":"2020","author":[{"given":"Elisa","family":"Banchi","sequence":"first","affiliation":[{"name":"Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy"},{"name":"Division of Oceanography, National Institute of Oceanography and Applied Geophysics, via Piccard 54, 34151, Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudio G","family":"Ametrano","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuele","family":"Greco","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Stankovi\u0107","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy"},{"name":"Marine Biology Station, National Institute of Biology, Forna\u010de 41, Piran, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Muggia","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"Pallavicini","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Trieste, via Giorgieri 5, 34127, Trieste, Italy"},{"name":"Division of Oceanography, National Institute of Oceanography and Applied Geophysics, via Piccard 54, 34151, Trieste, Italy"},{"name":"Department of Biology and Evoliution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,2,4]]},"reference":[{"key":"2020020405125755400_ref1","doi-asserted-by":"crossref","first-page":"2045","DOI":"10.1111\/j.1365-294X.2012.05470.x","article-title":"Towards next-generation biodiversity assessment using DNA metabarcoding","volume":"21","author":"Taberlet","year":"2012","journal-title":"Mol. 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Resour."},{"key":"2020020405125755400_ref9","first-page":"410829","article-title":"Temperate grass allergy season defined by spatio-temporal shifts in airborne pollen communities","author":"Brennan","year":"2018","journal-title":"bioRxiv"},{"key":"2020020405125755400_ref10","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0195403","article-title":"Plant DNA metabarcoding of lake sediments: how does it represent the contemporary vegetation","volume":"13","author":"Alsos","year":"2018","journal-title":"PloS One"},{"key":"2020020405125755400_ref11","doi-asserted-by":"crossref","first-page":"9858","DOI":"10.1021\/acs.jafc.8b02814","article-title":"Herbivore-diet analysis based on Illumina MiSeq sequencing: the potential use of an ITS2-barcoding approach to establish qualitative and quantitative predictions of diet composition of Mongolian sheep","volume":"66","author":"Guo","year":"2018","journal-title":"J. Agric. Food Chem."},{"key":"2020020405125755400_ref12","first-page":"1","article-title":"Evaluating the efficacy of sample collection approaches and DNA metabarcoding for identifying the diversity of plants utilized by nectivorous bats","volume":"999","author":"Edwards","year":"2018","journal-title":"Genome"},{"key":"2020020405125755400_ref13","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.foodcont.2018.04.040","article-title":"Comparative analysis of Illumina and ion torrent high-throughput sequencing platforms for identification of plant components in herbal teas","volume":"93","author":"Speranskaya","year":"2018","journal-title":"Food Control"},{"key":"2020020405125755400_ref14","doi-asserted-by":"crossref","DOI":"10.1007\/s10453-019-09574-2","article-title":"Relevance of plant and fungal DNA metabarcoding in aerobiology","author":"Banchi","year":"2019","journal-title":"Aerobiologia"},{"key":"2020020405125755400_ref15","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1093\/nar\/gky1022","article-title":"The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications","volume":"47","author":"Nilsson","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2020020405125755400_ref16","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/nar\/gkx855","article-title":"ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA internal transcribed spacer 1 (ITS1) sequences","volume":"46","author":"Santamaria","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020020405125755400_ref17","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. 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Resour."},{"key":"2020020405125755400_ref22","doi-asserted-by":"crossref","first-page":"19641","DOI":"10.1073\/pnas.1104551108","article-title":"Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants","volume":"108","author":"China Plant BOLD Group","year":"2011","journal-title":"PNAS"},{"key":"2020020405125755400_ref23","article-title":"Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species","volume":"5","author":"Chen","year":"2010","journal-title":"PloS One"},{"key":"2020020405125755400_ref24","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1111\/brv.12104","article-title":"Plant DNA barcoding: from gene to genome","volume":"90","author":"Li","year":"2015","journal-title":"Biol. 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