Descrição
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).
Registros de Dados
Os dados deste recurso de evento de amostragem foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 86 registros.
Também existem 1 tabelas de dados de extensão. Um registro de extensão fornece informações adicionais sobre um registro do núcleo. O número de registros em cada tabela de dados de extensão é ilustrado abaixo.
This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.
Versões
A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.
Como citar
Pesquisadores deveriam citar esta obra da seguinte maneira:
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
Direitos
Pesquisadores devem respeitar a seguinte declaração de direitos:
O editor e o detentor dos direitos deste trabalho é CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.
GBIF Registration
Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 5d859845-6734-4a30-bd1c-9d278f0e0e40. CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por GBIF Portugal.
Palavras-chave
Vascular plants; habitats; inventories; Reference database; Trás-os-montes; Portugal; DNA barcoding
Contatos
- Originador
- Project Coordinator
- Campus Agrário de Vairão
- Originador
- Junior Researcher
- Campus Agrário de Vairão
- Originador
- Plant taxonomist
- Campus Agrário de Vairão
- Originador
- Senior Researcher
- Campus Agrário de Vairão
- Originador
- Senior Researcher
- Campus Agrário de Vairão
- Originador
- Project co-coordinator
- Herdade da Mitra
- Originador
- Student
- Campus Agrário de Vairão
- Provedor Dos Metadados ●
- Originador
- Technician
- Campus Agrário de Vairão
- Provedor Dos Metadados
- Technician
- Quinta dos Prados
- Usuário
- Researcher
- Campus Agrário de Vairão
- Usuário
Cobertura Geográfica
The study was carried out in the Trás-os-Montes region, specifically in the districts of Bragança and Vila Real in northeastern Portugal.
| Coordenadas delimitadoras | Sul Oeste [41,336, -7,494], Norte Leste [41,832, -6,615] |
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Cobertura Taxonômica
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.
| Reino | Plantae |
|---|---|
| Filo | Tracheophyta |
| Class | Liliopsida, Lycopodiopsida, Magnoliopsida, Pinopsida, Polypodiopsida, Psilotopsida, Pteridopsida |
| Ordem | 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 |
| Família | 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 |
Cobertura Temporal
| Data Inicial / Data final | 2018-02-08 / 2020-07-06 |
|---|
Dados Sobre o Projeto
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.
| Título | The InBIO Barcoding Initiative Database: contribution to the knowledge of DNA barcodes of the vascular plants of northeastern Portugal |
|---|---|
| Identificador | The InBIO Barcoding Initiative Databases |
| Financiamento | 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). |
| Descrição da Área de Estudo | The region of Trás-os-Montes is located in the mountainous northeast of Portugal, comprising the districts of Vila Real and Bragança. |
| Descrição do 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. |
O pessoal envolvido no projeto:
- Autor
- Autor
- Autor
- Autor
- Autor
- Autor
- Autor
- Autor
- Autor
Métodos de Amostragem
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.
| Área de Estudo | 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. |
|---|---|
| Controle de Qualidade | 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 |
Descrição dos passos do método:
- 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.
Dados de Coleção
| Nome da Coleção | Plantas Vasculares - Herbário Português |
|---|---|
| Identificador da Coleção | Herbário da Universidade do Porto |
| Métodos de preservação do espécime | Seco |
|---|
| Unidades de Curadoria | Entre 72.113 e 72.772 sample |
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Metadados Adicionais
| Propósito | 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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| Descrição da manutenção | This resource will be regularly checked for accuracy. |
| Identificadores alternativos | http://ipt.gbif.pt/ipt/resource?r=iblt_plants_portugal |