Dataset Information

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

ABSTRACT:

Background

The use of DNA barcoding allows unprecedented advances in biodiversity assessments and monitoring schemes of freshwater ecosystems; nevertheless, it requires the construction of comprehensive reference collections of DNA sequences that represent the existing biodiversity. Plecoptera are considered particularly good ecological indicators and one of the most endangered groups of insects, but very limited information on their DNA barcodes is available in public databases. Currently, less than 50% of the Iberian species are represented in BOLD.

New information

The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera dataset contains records of 71 specimens of Plecoptera. All specimens have been morphologically identified to species level and belong to 29 species in total. This dataset contributes to the knowledge on the DNA barcodes and distribution of Plecoptera from the Iberian Peninsula and it is one of the IBI database public releases that makes available genetic and distribution data for a series of taxa.The species represented in this dataset correspond to an addition to public databases of 17 species and 21 BINs. Fifty-eight specimens were collected in Portugal and 18 in Spain during the period of 2004 to 2018. All specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources and their DNA barcodes are publicly available in the Barcode of Life Data System (BOLD) online database. The distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

SUBMITTER: Ferreira S

PROVIDER: S-EPMC7403161 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

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

Ferreira Sonia S Tierno de Figueroa José Manuel JM Martins Filipa Ms FM Verissimo Joana J Quaglietta Lorenzo L Grosso-Silva José Manuel JM Lopes Pedro B PB Sousa Pedro P Paupério Joana J Fonseca Nuno A NA Beja Pedro P

Biodiversity data journal 20200707

<h4>Background</h4>The use of DNA barcoding allows unprecedented advances in biodiversity assessments and monitoring schemes of freshwater ecosystems; nevertheless, it requires the construction of comprehensive reference collections of DNA sequences that represent the existing biodiversity. Plecoptera are considered particularly good ecological indicators and one of the most endangered groups of insects, but very limited information on their DNA barcodes is available in public databases. Current ...[more]

PMID: 32821214

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Project description:BackgroundBees are important actors in terrestrial ecosystems and are recognised for their prominent role as pollinators. In the Iberian Peninsula, approximately 1,100 bee species are known, with nearly 100 of these species being endemic to the Peninsula. A reference collection of DNA barcodes, based on morphologically identified bee specimens, representing 514 Iberian species, was constructed. The "InBIO Barcoding Initiative Database: DNA Barcodes of Iberian bees" dataset contains records of 1,059 sequenced specimens. The species of this dataset correspond to about 47% of Iberian bee species diversity and 21% of endemic species diversity. For peninsular Portugal only, the corresponding coverage is 71% and 50%. Specimens were collected between 2014 and 2022 and are deposited in the research collection of Thomas Wood (Naturalis Biodiversity Center, The Netherlands), in the FLOWer Lab collection at the University of Coimbra (Portugal), in the Andreia Penado collection at the Natural History and Science Museum of the University of Porto (MHNC-UP) (Portugal) and in the InBIO Barcoding Initiative (IBI) reference collection (Vairão, Portugal).New informationOf the 514 species sequenced, 75 species from five different families are new additions to the Barcode of Life Data System (BOLD) and 112 new BINs were added. Whilst the majority of species were assigned to a single BIN (94.9%), 27 nominal species were assigned to multiple BINs. Although the placement into multiple BINs may simply reflect genetic diversity and variation, it likely also represents currently unrecognised species-level diversity across diverse taxa, such as Amegillaalbigena Lepeletier, 1841, Andrenarussula Lepeletier, 1841, Lasioglossumleucozonium (Schrank, 1781), Nomadafemoralis Morawitz, 1869 and Sphecodesalternatus Smith, 1853. Further species pairs of Colletes, Hylaeus and Nomada were placed into the same BINs, emphasising the need for integrative taxonomy within Iberia and across the Mediterranean Basin more broadly. These data substantially contribute to our understanding of bee genetic diversity and DNA barcodes in Iberia and provide an important baseline for ongoing taxonomic revisions in the West Palaearctic biogeographical region.

Project description:BackgroundMetabarcoding is invaluable for understanding trophic interactions, enabling high-resolution and rapid dietary assessments. However, it requires a robust DNA barcode reference library for accurate taxa identification. This dataset has been generated in the framework of the InBIO Barcoding Initiative (IBI) and Agrivole project. The integration of these two projects was crucial, as Agrivole aimed to investigate the trophic niche of small mammals in Trás-os-Montes Region through DNA metabarcoding, which required a reliable plant DNA barcode library for this same region. Given the large number of species not yet represented in international databases, a survey of local plants was essential to fill this gap. Thus, this study created an accurate DNA reference database for the plants of the Trás-os-Montes Region of Portugal.New informationThe current DNA reference database contains 632 vascular plant samples, all morphologically identified and belonging to 435 species. This represents 14% and 38.7% of the total known plant species for Portugal and the study area, respectively.Of the 1781 barcode sequences provided in this dataset, 1099 contain new information (61.7%) at different levels: 254 (13.6%, ITS2: 41, trnL-ef: 126, trnL-gh: 87) are completely new to GenBank and/or BOLD databases at the time of publication, 438 (24.6%, ITS2: 59, trnL-ef: 173, trnL-gh: 206) are new records for a given species and 407 (22.9%, ITS2: 187, trnL-ef: 206, trnL-gh: 14) provide additional information (e.g. different bp length, intraspecific genetic variability); the remaining 682 sequences (38.3%) are equal (100% identity) to sequences already publicly available for the identified species. Overall, this dataset represents a significant contribution to the genetic knowledge of vascular plants represented in public libraries. This is one of the public releases of the IBI database, which provides genetic and distributional data for several taxa.All vouchers are deposited in the Herbarium of the Museum of Natural History and Science of the University of Porto (MHNC-UP) and their DNA barcodes are publicly available in the Barcode of Life Data System (BOLD), NCBI GenBank online databases and International Nucleotide Sequence Database Collaboration (INSDC).

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Dataset Information

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

Background

New information

Publications

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

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