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      The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees

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          Abstract

          Background

          Bees 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 information

          Of 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 Amegilla albigena Lepeletier, 1841, Andrena russula Lepeletier, 1841, Lasioglossum leucozonium (Schrank, 1781), Nomada femoralis Morawitz, 1869 and Sphecodes alternatus 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.

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          Most cited references77

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          VSEARCH: a versatile open source tool for metagenomics

          Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
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            bold: The Barcode of Life Data System (http://www.barcodinglife.org)

            The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.
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              obitools: a unix-inspired software package for DNA metabarcoding.

              DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: http://metabarcoding.org/obitools. A Galaxy wrapper is available on the GenOuest core facility toolshed: http://toolshed.genouest.org.
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                Author and article information

                Contributors
                Journal
                Biodivers Data J
                Biodivers Data J
                1
                urn:lsid:arphahub.com:pub:F9B2E808-C883-5F47-B276-6D62129E4FF4
                urn:lsid:zoobank.org:pub:245B00E9-BFE5-4B4F-B76E-15C30BA74C02
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2836
                1314-2828
                2024
                05 March 2024
                : 12
                : e117172
                Affiliations
                [1 ] Naturalis Biodiversity Center, Leiden, Netherlands Naturalis Biodiversity Center Leiden Netherlands
                [2 ] Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra Portugal
                [3 ] University of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000, Mons, Belgium University of Mons, Research Institute for Biosciences, Laboratory of Zoology, Place du parc 20, 7000 Mons Belgium
                [4 ] Ciência Viva - Agência Nacional para a Cultura Científica e Tecnológica, Largo José Mariano Gago n.º1, Parque das Nações, 1990-073, Lisboa, Portugal Ciência Viva - Agência Nacional para a Cultura Científica e Tecnológica, Largo José Mariano Gago n.º1, Parque das Nações, 1990-073 Lisboa Portugal
                [5 ] BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão, Vila do Conde, Portugal BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485–661 Vairão Vila do Conde Portugal
                [6 ] CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Vila do Conde, Portugal CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão Vila do Conde Portugal
                [7 ] University of Mons, Bruxelles, Belgium University of Mons Bruxelles Belgium
                [8 ] EBM, Estação Biológica de Mertola, Praça Luis de Camoes, Mertola, Mertola, Portugal EBM, Estação Biológica de Mertola, Praça Luis de Camoes, Mertola Mertola Portugal
                Author notes
                Corresponding author: Sónia Ferreira ( soniaferreira@ 123456cibio.up.pt ).

                Academic editor: Dominique Zimmermann

                Author information
                https://orcid.org/0000-0001-5653-224X
                https://orcid.org/0000-0001-5448-8396
                https://orcid.org/0000-0002-6868-7035
                https://orcid.org/0000-0003-3005-9030
                https://orcid.org/0000-0001-8880-1838
                https://orcid.org/0000-0002-7358-6685
                https://orcid.org/0000-0002-9068-3954
                https://orcid.org/0000-0001-8164-0760
                https://orcid.org/0000-0002-6884-3966
                Article
                117172 23402
                10.3897/BDJ.12.e117172
                10933585
                38481855
                ad21a8fa-a93b-414f-847c-6abcd5c9940f
                Thomas James Wood, Hugo Gaspar, Romain Le Divelec, Andreia Penado, Teresa Luísa Silva, Vanessa A. Mata, Joana Veríssimo, Denis Michez, Sílvia Castro, João Loureiro, Pedro Beja, Sónia Ferreira

                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
                : 11 December 2023
                : 14 February 2024
                Page count
                Figures: 2, Tables: 2, References: 78
                Categories
                Data Paper (Biosciences)
                Hymenoptera
                Molecular biology
                Zoology & Animal Biology
                Systematics
                Biodiversity & Conservation
                Western Europe

                hymenoptera,occurrence records,species distributions,peninsular portugal,peninsular spain,dna barcode,cytochrome c oxidase subunit i (coi),pollinator

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