Description
This dataset contains 659 occurrence records of vascular plants from the Trás-os-Montes region of northeastern Portugal, of which 647 were morphologically identified to the most specific taxon (species, subspecies or variety), comprising 448 species belonging to 69 families. The samples were collected as part of the Agrivole project, in collaboration with the InBIO Barcoding Initiative (IBI), to build a reference collection of DNA barcodes for the region. Vascular plants were collected from traditionally managed olive grove agroecosystems and their surrounding areas during August 2018, May–June 2019 and June 2020, herborized in situ and a leaf tissue sample was collected for DNA extraction. Specimens were identified and revised by experts in vascular plant taxonomy. Sequencing was carried out for three molecular markers, TrnL (gh and ef) and ITS2, and all obtained DNA sequences were submitted to BOLD (Barcode of Life Data System) and GenBank databases. Specimens are deposited in the herbarium of the Natural History and Science Museum of the University of Porto (MHNC-UP).
Enregistrements de données
Les données de cette ressource données d'échantillonnage ont été publiées sous forme d'une Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant qu'ensemble d'un ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 86 enregistrements.
1 tableurs de données d'extension existent également. Un enregistrement d'extension fournit des informations supplémentaires sur un enregistrement du cœur de standard (core). Le nombre d'enregistrements dans chaque tableur de données d'extension est illustré ci-dessous.
Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.
Versions
Le tableau ci-dessous n'affiche que les versions publiées de la ressource accessibles publiquement.
Comment citer
Les chercheurs doivent citer cette ressource comme suit:
Queirós J, Silva R, Pinho C J, Vale-Gonçalves H, Pita R, Alves P C, Beja P, Paupério J, Porto M (2024). The InBIO Barcoding Initiative Database: contribution to the knowledge of DNA barcodes of the vascular plants of northeastern Portugal. Version 1.0. CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal. Samplingevent dataset. http://ipt.gbif.pt/ipt/resource?r=iblt_plants_portugal&v=1.0
Droits
Les chercheurs doivent respecter la déclaration de droits suivante:
L’éditeur et détenteur des droits de cette ressource est CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.
Enregistrement GBIF
Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 5d859845-6734-4a30-bd1c-9d278f0e0e40. CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du GBIF Portugal.
Mots-clé
Vascular plants; habitats; inventories; Reference database; Trás-os-montes; Portugal; DNA barcoding
Contacts
- Créateur
- Project Coordinator
- Campus Agrário de Vairão
- Créateur
- Junior Researcher
- Campus Agrário de Vairão
- Créateur
- Plant taxonomist
- Campus Agrário de Vairão
- Créateur
- Senior Researcher
- Campus Agrário de Vairão
- Créateur
- Senior Researcher
- Campus Agrário de Vairão
- Créateur
- Project co-coordinator
- Herdade da Mitra
- Créateur
- Student
- Campus Agrário de Vairão
- Fournisseur Des Métadonnées ●
- Créateur
- Technician
- Campus Agrário de Vairão
- Fournisseur Des Métadonnées
- Technician
- Quinta dos Prados
- Utilisateur
- Researcher
- Campus Agrário de Vairão
- Utilisateur
Couverture géographique
The study was carried out in the Trás-os-Montes region, specifically in the districts of Bragança and Vila Real in northeastern Portugal.
| Enveloppe géographique | Sud Ouest [41,336, -7,494], Nord Est [41,832, -6,615] |
|---|
Couverture taxonomique
A total of 659 specimens were collected, of which 647 were morphologically identified to the most specific taxon (species, subspecies or variety). This data set includes 448 species belonging to 69 families, 34 orders, 7 classes and 1 phylum.
| Kingdom | Plantae |
|---|---|
| Phylum | Tracheophyta |
| Class | Liliopsida, Lycopodiopsida, Magnoliopsida, Pinopsida, Polypodiopsida, Psilotopsida, Pteridopsida |
| Order | Apiales, Asparagales, Asterales, Boraginales, Brassicales, Caryophyllales, Cucurbitales, Dioscoreales, Dipsacales, Equisetales, Ericales, Fabales, Fagales, Gentianales, Geraniales, Isoetales, Lamiales, Malpighiales, Malvales, Myrtales, Ophioglossales, Pinales, Piperales, Poales, Polypodiales, Pteridales, Ranunculales, Rosales, Santalales, Sapindales, Saxifragales, Solanales, Zygophyllales |
| Family | Amaranthaceae, Amaryllidaceae, Anacardiaceae, Apiaceae, Aristolochiaceae, Asparagaceae, Aspleniaceae, Asteraceae, Boraginaceae, Brassicaceae, Campanulaceae, Cannabaceae, Caprifoliaceae, Caryophyllaceae, Cistaceae, Convolvulaceae, Crassulaceae, Cucurbitaceae, Cupressaceae, Cyperaceae, Cytinaceae, Dennstaedtiaceae, Dioscoreaceae, Equisetaceae, Ericaceae, Euphorbiaceae, Fabaceae, Fagaceae, Gentianaceae, Geraniaceae, Hypericaceae, Isoetaceae, Juglandaceae, Juncaceae, Lamiaceae, Linaceae, Lythraceae, Malvaceae, Montiaceae, Oleaceae, Onagraceae, Ophioglossaceae, Orchidaceae, Orobanchaceae, Paeoniaceae, Papaveraceae, Plantaginaceae, Plumbaginaceae, Poaceae, Polygalaceae, Polygonaceae, Portulacaceae, Primulaceae, Pteridaceae, Ranunculaceae, Resedaceae, Rosaceae, Rubiaceae, Rutaceae, Salicaceae, Santalaceae, Saxifragaceae, Scrophulariaceae, Solanaceae, Thymelaeaceae, Urticaceae, Verbenaceae, Violaceae, Zygophyllaceae |
Couverture temporelle
| Date de début / Date de fin | 2018-02-08 / 2020-07-06 |
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Données sur le projet
This dataset contains 659 occurrence records of vascular plants from the Trás-os-Montes region of northeastern Portugal, of which 647 were morphologically identified to the most specific taxon (species, subspecies or variety), comprising 448 species belonging to 69 families. The samples were collected as part of the Agrivole project, in collaboration with the InBIO Barcoding Initiative (IBI), to build a reference collection of DNA barcodes for the region. Vascular plants were collected from traditionally managed olive grove agroecosystems and their surrounding areas during August 2018, May–June 2019 and June 2020, herborized in situ and a leaf tissue sample was collected for DNA extraction.
| Titre | The InBIO Barcoding Initiative Database: contribution to the knowledge of DNA barcodes of the vascular plants of northeastern Portugal |
|---|---|
| Identifiant | The InBIO Barcoding Initiative Databases |
| Financement | This work was funded by the European Regional Development Fund (ERDF) through “Programa Operacional de Factores de Competitividade—COMPETE” and by national funds through FCT—Portuguese Foundation for Science and Technology, IP, under the scope of the project AGRIVOLE (PTDC/BIA- ECO/31728/2017). |
| Description du domaine d'étude / de recherche | The region of Trás-os-Montes is located in the mountainous northeast of Portugal, comprising the districts of Vila Real and Bragança. |
| Description du design | Vascular plants were collected from traditionally managed olive grove agroecosystems and surrounding areas in northeastern Portugal. Each distinct vascular plant species within each patch was collected, photographed and then herbarized in situ. These were then morphologically identified by experts and a portion of the leaf tissue was used to obtain DNA barcodes. |
Les personnes impliquées dans le projet:
- Auteur
- Auteur
- Auteur
- Auteur
- Auteur
- Auteur
- Auteur
- Auteur
- Auteur
Méthodes d'échantillonnage
Plant samples were collected in the northeast of Portugal from traditionally managed olive grove agroecosystems and their surrounding areas. Young olive groves were used as a central point from which a 50m buffer zone was drawn. Every distinct vascular plant species within each patch was collected, photographed, and then herbarised in situ with an assigned specimen number. A portion of leaf tissue was collected from each sample, placed in a paper envelope, and then stored in a zip-lock bag with silica gel until DNA extraction. To minimise contamination between samples, tweezers and scissors were systematically sterilised with 100% ethanol under flame. After morphological identification, all the specimens (vouchers) were deposited in the herbarium of the Natural History and Science Museum of the University of Porto (MHNC-UP) with the codes PO-V72113–PO-V72772.
| Etendue de l'étude | The data were collected in the Trás-os-Montes region (Northeast Portugal), in the municipalities of Aljó, Bragança, Vila Real, Macedo de Cavaleiros, Vila Flor and Vimioso. |
|---|---|
| Contrôle qualité | Collected samples were identified and revised by experts in vascular plant taxonomy. The obtained DNA barcode sequences were compared against the GenBank and BOLD databases, and the top hits were examined to identify potential PCR/ sequencing errors, contaminations or misidentifications.item-0item-0 |
Description des étapes de la méthode:
- 1. Vascular plants were collected in the northeast of Portugal in August 2018, May–June 2019 and June 2020, from traditionally managed olive grove agroecosystems and their surrounding areas. A leaf tissue sample was collected for DNA extraction. 2. Taxonomic identification was carried out, after herborisation, under a stereomicroscope, using mainly the dichotomous keys of Flora Iberica. For some specimens, it was necessary to consult other works namely in cases of possible hybrids, or in cases where the Flora Iberica has a different treatment of the taxon of interest. Whenever possible, the specimens were identified at the infraspecific level. 3. DNA extracts were obtained from collected leaf tissues and DNA barcodes were sequenced using Illumina protocols for two regions: the chloroplast trnL (UAA) intron region (markers e/ f: 147–540 bp and g/ h:10–143 bp) and the nuclear internal transcribed spacer 2 region, ITS2 (marker UniPlantF/ UniPlantR: 187–387 bp). 4. Sequences were submitted to BOLD and GenBank databases.
Données de collection
| Nom de la collection | Plantas Vasculares - Herbário Português |
|---|---|
| Identifiant de collection | Herbário da Universidade do Porto |
| Méthode de conservation des spécimens | Dried |
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| Unités de conservation | Entre (nombre minimal) 72 113 et (nombre maximal) 72 772 sample |
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Métadonnées additionnelles
| Objet | This dataset was generated as part of the Agrivole project, in collaboration with the InBIO Barcoding Initiative (IBI), which aimed to investigate the impact of small mammals, particularly voles, in local agroecosystems. The project aimed to explore the trophic niche of these small mammals through DNA metabarcoding analysis of their faeces using high throughput sequencing methods. This required a reliable plant DNA barcoding library for the region to accurately and precisely infer the dietary taxa consumed by each species, for which collaboration with IBI was crucial. Therefore, this database aims to provide a reference database of DNA barcodes of the vascular plants of the Trás-os-Montes region in northeastern Portugal. This library will facilitate the DNA-based identification of plant species for the Agrivole project and other DNA metabarcoding and traditional molecular studies. |
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| Description de la fréquence de mise à jour | This resource will be regularly checked for accuracy. |
| Identifiants alternatifs | http://ipt.gbif.pt/ipt/resource?r=iblt_plants_portugal |