Establishing reliable DNA barcoding primers for jumping plant lice (Psylloidea, Hemiptera)

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Abstract

Objectives

DNA Barcoding has proven to be a reliable method for rapid insect identification. The success of this method is based on the amplification of a specific region, the ‘Folmer’ barcode region at the 5´ start of the cytochrome c oxidase 1 gene (cox1), with universal primers. Previous studies showed failures of standard “universal” primers to amplify this region in psyllids. The aim of the study was the design of a new alternative more reliable primer combination for taxa of the superfamily Psylloidea and its comparison with the performance of the standard “universal” Folmer-primers.

Results

A newly designed degenerate forward primer LCOP-F was developed following comparison of the sequence alignment of the priming site of “universal” primer LCO1490 and the standard insect forward primer LepF1. When combined with the “universal” reverse primer, HCO2198, this new primer pairing was able to generate barcode sequence for all 36 species in 20 genera across the five families of psyllids tested in this study, and these primers were found to be more universally reliable across psyllid taxa than other primer pairs tested.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-023-06585-8.

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Most cited references 34

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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.

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Biological identifications through DNA barcodes.

Paul Hebert, Alina Cywinska, Shelley Ball … (2003)

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

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bold: The Barcode of Life Data System (http://www.barcodinglife.org)

Sujeevan Ratnasingham, Paul Hebert (2007)

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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Author and article information

Contributors

Felipe Siverio:

ORCID: http://orcid.org/0000-0002-8886-414X

fsiverio@icia.es

Journal

Journal ID (nlm-ta): BMC Res Notes

Journal ID (iso-abbrev): BMC Res Notes

Title: BMC Research Notes

Publisher: BioMed Central (London )

ISSN (Electronic): 1756-0500

Publication date (Electronic): 8 November 2023

Publication date PMC-release: 8 November 2023

Publication date Collection: 2023

Volume: 16

Electronic Location Identifier: 322

Affiliations

[1 ]Instituto Canario de Investigaciones Agrarias, Unidad de Protección Vegetal, ( https://ror.org/05hxzkx81) C/ El Boquerón s/n, 38270 La Laguna, Tenerife Spain

[2 ]Universidad de La Laguna, ( https://ror.org/01r9z8p25) Avda. Astrofísico Francisco Sánchez, SN. Edificio Calabaza-AN.2D Apdo. 456., 38200 La Laguna, Tenerife Spain

[3 ]Botany Department and Biodiversity Research Centre, University of British Columbia, ( https://ror.org/03rmrcq20) Vancouver, BC Canada

Author information

Saskia Bastin http://orcid.org/0000-0001-9307-7223

Diana M. Percy http://orcid.org/0000-0002-0468-2892

Felipe Siverio http://orcid.org/0000-0002-8886-414X

Article

Publisher ID: 6585

DOI: 10.1186/s13104-023-06585-8

PMC ID: 10634070

PubMed ID: 37941051

SO-VID: 9fd638e8-7e62-4c7b-b808-6fed07c18b3f

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 28 May 2023

Date accepted : 20 October 2023

Funding

Funded by: Agencia Canaria de Investigación, Innovación y Sociedad de la Información (ACIISI)

Award ID: 2019-2023 PhD

Funded by: PROGRAMA MAC 2014-2020 - INTERREG

Award ID: CUARENTAGRI (MAC2/1.1a/231)

Custom metadata

ScienceOpen disciplines: Medicine

Keywords: psyllids,molecular identification,primer efficacy,species identification,coi barcode,standard barcode

Data availability:

ScienceOpen disciplines: Medicine

Keywords: psyllids, molecular identification, primer efficacy, species identification, coi barcode, standard barcode

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Establishing reliable DNA barcoding primers for jumping plant lice (Psylloidea, Hemiptera)

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Abstract

Objectives

Results

Supplementary Information

Related collections

Karger: Nephrology

Most cited references 34

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Biological identifications through DNA barcodes.

bold: The Barcode of Life Data System (http://www.barcodinglife.org)

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