The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese  Diptera  01

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Abstract

Background

The InBIO Barcoding Initiative (IBI) Diptera 01 dataset contains records of 203 specimens of Diptera . All specimens have been morphologically identified to species level, and belong to 154 species in total. The species represented in this dataset correspond to about 10% of continental Portugal dipteran species diversity. All specimens were collected north of the Tagus river in Portugal. Sampling took place from 2014 to 2018, and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.

New information

This dataset contributes to the knowledge on the DNA barcodes and distribution of 154 species of Diptera from Portugal and is the first of the planned IBI database public releases, which will make available genetic and distribution data for a series of taxa. All specimens have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD) online database and the distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

Related collections

Most cited references 14

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Use of DNA barcodes to identify flowering plants.

W. John Kress, Kenneth J Wurdack, Elizabeth Zimmer … (2005)

Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

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Is Open Access

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Hannah Weigand, Arne J. Beermann, Fedor Čiampor … (2019)

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DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

Mari Kekkonen, Paul Hebert (2014)

The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.

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Author and article information

Contributors

Sonia A Ferreira:

ORCID: https://orcid.org/0000-0002-6884-3966

Journal

Journal ID (nlm-ta): Biodivers Data J

Journal ID (iso-abbrev): Biodivers Data J

Journal ID (publisher-id): 1

Journal ID (index): urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4

Journal ID (aggregator): urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02

Title: Biodiversity Data Journal

Publisher: Pensoft Publishers

ISSN (Print): 1314-2836

ISSN (Electronic): 1314-2828

Publication date Collection: 2020

Publication date (Electronic): 20 March 2020

Volume: 8

Electronic Location Identifier: e49985

Affiliations

[1 ] CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Vila do Conde, Portugal CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão Vila do Conde Portugal

[2 ] Rua Calouste Gulbenkian 237 4H3, 4050-145, Porto, Portugal Rua Calouste Gulbenkian 237 4H3, 4050-145 Porto Portugal

[3 ] Computational Biology and Population Genomics Group, cE3c, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal Computational Biology and Population Genomics Group, cE3c, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa Portugal

[4 ] CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa Portugal

Author notes

Corresponding author: Sonia A Ferreira ( hiporame@ 123456gmail.com ).

Academic editor: Torsten Dikow

Author information

Sonia A Ferreira https://orcid.org/0000-0002-6884-3966

Pedro Sousa https://orcid.org/0000-0002-5859-9656

Joana Paupério https://orcid.org/0000-0003-2569-0768

Nuno A Fonseca https://orcid.org/0000-0003-4832-578X

Article

Publisher ID: 49985 Publisher-manuscript ID: 13096

DOI: 10.3897/BDJ.8.e49985

PMC ID: 7101446

SO-VID: e4bda248-9185-4a20-9082-becc862bee7c

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 08 January 2020

Date accepted : 21 February 2020

Page count

Figures: 3, Tables: 2, References: 23

Funding

This project has received funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 668981 and by the project PORBIOTA—Portuguese E-Infrastructure for Information and Research on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER), by EDP Biodiversity Chair, and is part of research conducted at the Long Term Research Site of Baixo Sabor (LTER_EU_PT_002). P.S. was funded by the project ECOLIVES – Fostering sustainable management in Mediterranean olive farms: pest control services provided by wild species as incentives for biodiversity conservation (PTDC/AAG-REC/6480/2014/) supported by Portuguese national funds by FCT/MCTES and co-financed by Fundo Europeu de Desenvolvimento Regional (FEDER) throughout COMPETE – Programa Operacional Factores de Competitividade (POFC).

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The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01

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Abstract

Background

New information

Related collections

Pensoft Biodiversity

Most cited references 14

Use of DNA barcodes to identify flowering plants.

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

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Contributors

Journal

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Author notes

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Article

History

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Funding

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