The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera

Sónia Ferreira; J. Manuel Tierno de Figueroa; Filipa M S Martins; Joana Veríssimo; Lorenzo Quaglietta; José M. Grosso-Silva; Pedro Brito Lopes; Pedro Sousa; Pedro Beja

doi:10.15468/3vkdr2

The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera

Citation

Ferreira S, Tierno de Figueroa J M, Martins F M S, Veríssimo J, Quaglietta L, Grosso-Silva J M, Lopes P B, Sousa P, Beja P (2021). The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera. Version 1.6. CIBIO (Research Center in Biodiversity and Genetic Resources) Portugal. Occurrence dataset https://doi.org/10.15468/3vkdr2 accessed via GBIF.org on 2024-12-11.

Description

The dataset contains 71 records of Plecoptera specimens collected from 2004 to 2018 in the Iberian Peninsula (Ferreira et al., 2020). Twenty-nine stoneflies species are represented in the dataset, contributing to the knowledge on the DNA barcodes and distribution of the Plecoptera in Iberia. Specimens were captured during fieldwork directed specifically for the sampling of Plecoptera using different methodologies and stored in 96% ethanol. All specimens were morphologically identified to species level. A tissue sample, usually a leg, was collected from each individual, from which DNA was extracted. The DNA barcoding of these specimens was conducted within the InBIO Barcoding Initiative (IBI), funded by EnvMetaGen and PORBIOTA projects. DNA barcode sequences were deposited in BOLD (Barcode of Life Data System) online database. Preserved specimens and DNA extracts are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources).

Purpose

The InBIO Barcoding Initiative (IBI) aims to develop a reference collection of DNA barcoding sequences primarily covering Portuguese invertebrate taxa providing a tool in ecological studies.

Sampling Description

Study Extent

Iberian Peninsula.

Sampling

The studied material was collected in 40 different localities from Iberian Peninsula. Sampling was conducted between 2004 and 2018 on a wide range of habitats, using mainly hand-held sweep-nets or direct search for specimens. Collected specimens were examined in ethanol using a binocular stereoscopic microscope, and they were stored in 96% ethanol for downstream molecular analysis. Morphological identification was performed using keys and descriptions from literature (mainly Tierno de Figueroa et al. 2003 , Tierno de Figueroa et al. 2015).

Quality Control

All DNA barcodes sequences were compared against the BOLD database and the 99 top hits were inspected in order to detect possible issues due to contaminations or misidentifications. Prior submission to GBIF, data was checked for errors and inconsistencies with OpenRefine 3.2 (http://openrefine.org).

Method steps

Specimens were collected in 40 different localities of the Iberian Peninsula. Fieldwork was carried out from 2004 to 2018.
Specimens were collected during fieldwork by direct search of specimens on rocks and vegetation of streams and river margins, and in the use of entomological nets to intercept specimens flight. Collected specimens were stored in 96% ethanol.
Specimens were morphologically identified with the assistance of a stereoscopic microscope and using the available literature.
DNA barcodes were sequenced from all specimens. For this, one leg was removed from each individual, DNA was then extracted, and a 658 bp COI DNA barcode fragment was amplified and sequenced. Specimens and DNA extracts were deposited in the IBI reference collection at CIBIO (Research Center in Biodiversity and Genetic Resources).
All obtained sequences were submitted to BOLD and GenBank databases. The morphological identification of each sequenced specimen was contrasted with the results of the BLAST of the newly generated DNA barcodes in the BOLD Identification Engine.
Data was submitted to GBIF, after being checked for errors and inconsistencies with OpenRefine 3.3 (http://openrefine.org/).

Taxonomic Coverages

This dataset is composed of data relating to 71 Plecoptera specimens. All specimens were determined to species level. Overall, 29 species are represented in the dataset. These species belong to 16 genera and 7 families.

Animalia
rank: kingdom
Arthropoda
rank: phylum
Insecta
rank: class
Plecoptera
rank: order
Capniidae
rank: family
Chloroperlidae
rank: family
Leuctridae
rank: family
Nemouridae
rank: family
Perlidae
rank: family
Perlodidae
rank: family
Taeniopterygidae
rank: family

Geographic Coverages

Iberian Peninsula

Bibliographic Citations

Tierno de Figueroa J, Sánchez-Ortega A, Membiela-Iglesia P, Luzón-Ortega J (2003). Plecoptera. Fauna Ibérica. CSIC, Madrid, 404 pp. -
Tierno de Figueroa J, Luzón-Ortega J, López-Rodríguez M (2015) Orden Plecoptera. In: IBERFAUNA. El Banco de Datos de la Fauna Ibérica. Museo Nacional de Ciencias Naturales (CSIC). http://iberfauna.mncn.csic.es/showficha.aspx?rank=J&idtax=571. Accessed on: 2020-4-09. -
Ferreira, S., Tierno de Figueroa, J.M., Martins, F.M., Verissimo, J., Quaglietta, L., Grosso-Silva, J.M., Lopes, P.B., Sousa, P., Paupério, J., Fonseca, N.A. & Beja, P. (2020). The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera. Biodiversity Data Journal, 8: e55137. https://doi.org/10.3897/BDJ.8.e55137 -

Contacts

Sónia Ferreira
originator
position: Post-Doc Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: hiporame@gmail.com
userId: http://orcid.org/0000-0002-6884-3966

J. Manuel Tierno de Figueroa
originator
position: Full Professor
Universidad de Granada
ES
userId: http://orcid.org/0000-0003-1616-9815

Filipa M S Martins
originator
position: PhD student
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
email: filipamsmartins@gmail.com
userId: http://orcid.org/0000-0003-4191-5031

Joana Veríssimo
originator
position: PhD student
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
email: joana.filipa.verissimo@gmail.com
userId: http://orcid.org/0000-0002-8721-9376

Lorenzo Quaglietta
originator
position: Post-Doc Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
email: lorenzo.quaglietta@cibio.up.pt
userId: http://orcid.org/0000-0002-9703-0171

José M. Grosso-Silva
originator
position: Entomology Curator
Museu de História Natural e da Ciência da Universidade do Porto
PT
email: jmgrossosilva@gmail.com
userId: http://orcid.org/0000-0002-1094-0771

Pedro Brito Lopes
originator
position: Researcher
Rua do Torgal, nº 16 (Trigais)
Covilhã
PT
userId: http://orcid.org/0000-0002-5078-0602

Pedro Sousa
originator
position: Post-Doc Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: psousa@cibio.up.pt
userId: http://orcid.org/0000-0002-5859-9656

Pedro Beja
originator
position: Coordinating Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: pbeja@cibio.up.pt
userId: http://orcid.org/0000-0001-8164-0760

Sónia Ferreira
metadata author
position: Post-Doc Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: hiporame@gmail.com
userId: http://orcid.org/0000-0002-6884-3966

J. Manuel Tierno de Figueroa
metadata author
position: Full Professor
Universidad de Granada
ES
email: jmtdef@ugr.es
userId: http://orcid.org/0000-0003-1616-9815

Filipa M S Martins
metadata author
position: PhD student
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
email: filipamsmartins@gmail.com
userId: http://orcid.org/0000-0003-4191-5031

Joana Veríssimo
metadata author
position: PhD student
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
email: joana.filipa.verissimo@gmail.com
userId: http://orcid.org/0000-0002-8721-9376

Lorenzo Quaglietta
metadata author
position: Post-Doc Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: lorenzo.quaglietta@cibio.up.pt
userId: http://orcid.org/0000-0002-9703-0171

José M. Grosso-Silva
metadata author
position: Entomology Curator
Museu de História Natural e da Ciência da Universidade do Porto
PT
email: jmgrossosilva@gmail.com
userId: http://orcid.org/0000-0002-1094-0771

Pedro Brito Lopes
metadata author
position: Researcher
Rua do Torgal, nº 16 (Trigais)
Covilhã
PT
email: pedro.lopes275@gmail.com
userId: http://orcid.org/0000-0002-5078-0602

Pedro Sousa
metadata author
position: Post-Doc Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: psousa@cibio.up.pt
userId: http://orcid.org/0000-0002-5859-9656

Pedro Beja
metadata author
position: Coordinating Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: pbeja@cibio.up.pt
userId: http://orcid.org/0000-0001-8164-0760

Pedro Beja
administrative point of contact
position: Coordinating Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: pbeja@cibio.up.pt
userId: http://orcid.org/0000-0001-8164-0760

Sónia Ferreira
administrative point of contact
position: Post-Doc Researcher
CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto
PT
Telephone: +351 252660411
email: hiporame@gmail.com
userId: http://orcid.org/0000-0002-6884-3966