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Tiny insects, big troubles: a review of BOLD's COI database for Thysanoptera (Insecta)

Published online by Cambridge University Press:  24 August 2023

Mariana F. Lindner Open the ORCID record for Mariana F. Lindner [Opens in a new window] ,
Leonardo T. Gonçalves Open the ORCID record for Leonardo T. Gonçalves [Opens in a new window] ,
Filipe M. Bianchi Open the ORCID record for Filipe M. Bianchi [Opens in a new window] ,
Augusto Ferrari Open the ORCID record for Augusto Ferrari [Opens in a new window]  and
Adriano Cavalleri Open the ORCID record for Adriano Cavalleri [Opens in a new window]
Mariana F. Lindner*
Affiliation:
Department of Zoology, Laboratório de Entomologia Sistemática, Institute of Biosciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
Leonardo T. Gonçalves
Affiliation:
Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
Filipe M. Bianchi
Affiliation:
Department of Zoology, Laboratório de Entomologia Sistemática, Institute of Biosciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
Augusto Ferrari
Affiliation:
Laboratório de Entomologia, Sistemática e Biogeografia (LESB), Matéria Zoologia, Institute of Biological Sciences, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
Adriano Cavalleri
Affiliation:
Laboratório de Entomologia, Sistemática e Biogeografia (LESB), Matéria Zoologia, Institute of Biological Sciences, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, Brazil
*
Corresponding author: Mariana F. Lindner; Email: mflindner@hotmail.com
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Abstract

DNA Barcoding is an important tool for disciplines such as taxonomy, phylogenetics and phylogeography, with Barcode of Life Data System (BOLD) being the largest database of partial cytochrome c oxidase subunit I (COI) sequences. We provide the first extensive revision of the information available in this database for the insect order Thysanoptera, to assess: how many COI sequences are available; how representative these sequences are for the order; and the current potential of BOLD as a reference library for specimen identification and species delimitation. The COI database at BOLD currently represents only about 5% of the over 6400 valid thrips species, with a heavy bias towards a few species of economic importance. Clear Barcode gaps were observed for 24 out of 33 genera evaluated, but many outliers were also observed. We suggest that the COI sequences available in BOLD as a reference would not allow for accurate identifications in about 30% of Thysanoptera species in this database, which rises to 40% of taxa within Thripidae, the most sampled family within the order. Thus, we call for caution and a critical evaluation in using BOLD as a reference library for thrips Barcodes, and future efforts should focus on improving the data quality of this database.

Keywords

AeolothripidaeBarcode gapDNA BarcodingFrankliniellaPhlaeothripidaeThripidae
Type
Research Paper
Information
Bulletin of Entomological Research , Volume 113 , Issue 5 , October 2023 , pp. 703 - 715
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Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press

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References

Badotti, F., de Oliveira, F.S., Garcia, C F., Vaz, A.B.M., Fonseca, P.L.C., Nahum, L.A., Oliveira, G. and Góes-Neto, A. (2017) Effectiveness of ITS and sub-regions as DNA Barcode markers for the identification of Basidiomycota (Fungi). BMC Microbiology 17, 42.CrossRefGoogle ScholarPubMed
Bianchi, F.M. and Gonçalves, L.T. (2021a) Borrowing the Pentatomomorpha tome from the DNA Barcode library: scanning the overall performance of cox1 as a tool. Journal of Zoological Systematics and Evolutionary Research 59, 992–1012.CrossRefGoogle Scholar
Bianchi, F.M. and Gonçalves, L.T. (2021b) Getting science priorities straight: how to increase the reliability of specimen identification? Biology Letters 17, 1–4.CrossRefGoogle ScholarPubMed
BOLD - Barcode of Life Data System V4 (2023). Available at https://www.boldsystems.org/index.php. Last accessed in May 2023.Google Scholar
Cavalleri, A and Mound, LA (2012) Toward the identification of Frankliniella species in Brazil (Thysanoptera, Thripidae). Zootaxa 3270, 1–30.CrossRefGoogle Scholar
Chakraborty, R., Singha, D., Kumar, V., Pakrashi, A., Kundu, S., Chandra, K., Patnaik, S. and Tyagi, K. (2019) DNA Barcoding of selected Scirtothrips species (Thysanoptera) from India. Mitochondrial DNA Part B 4, 2710–2714.CrossRefGoogle ScholarPubMed
Collins, R.A. and Cruickshank, R.H. (2012) The seven deadly sins of DNA Barcoding. Molecular Ecology Resources 13, 969–975.CrossRefGoogle ScholarPubMed
Collins, R.A., Boykin, L.M., Cruickshank, R.H. and Armstrong, K.F. (2012) Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification. Methods in Ecology and Evolution 3, 457–465.CrossRefGoogle Scholar
Dickey, A.M., Kumar, V., Hoddle, M.S., Funderburk, J.E., Morgan, J.K., Jara-Cavieres, A., Shatters, R.G. Jr., Osborne, L.S. and McKenzie, C.L. (2015) The Scirtothrips dorsalis species complex: endemism and invasion in a global pest. PLoS ONE 10, e0123747.CrossRefGoogle Scholar
Erickson, D.L., Spouge, J., Resch, A., Weigt, L.A. and Kress, J.W. (2008) DNA Barcoding in land plants: developing standards to quantify and maximize success. Taxon 57, 1304–1316.CrossRefGoogle ScholarPubMed
Ghosh, A., Jangra, S., Dietzgen, R.G. and Yeh, W.-B. (2021) Frontiers approaches to the diagnosis of Thrips (Thysanoptera): how effective are the molecular and electronic detection platforms? Insects 12, 1–26.CrossRefGoogle Scholar
Gonçalves, L.T., Bianchi, F.M., Deprá, M. and Calegaro-Marques, C. (2021) Barcoding a can of worms: testing cox1 performance as a DNA Barcode of Nematoda. Genome 64, 705–717.CrossRefGoogle Scholar
Gonçalves, L.T., Françoso, E. and Deprá, M. (2022) Shorter, better, faster, stronger? Comparing the identification performance of full-length and mini-DNA Barcodes for apid bees (Hymenoptera: Apidae). Apidologie 53, 55. https://doi.org/10.1007/s13592-022-00958-xCrossRefGoogle Scholar
Hebert, P.D.N., Cywinska, A., Ball, S.L. and deWaard, J.R. (2003) Biological identifications through DNA Barcodes. Proceedings of the Royal Society B 270, 313–321.CrossRefGoogle ScholarPubMed
Iftikhar, R., Ashfaq, M., Rasool, A. and Hebert, P.D.N. (2016) DNA Barcode analysis of thrips (Thysanoptera) diversity in Pakistan reveals cryptic species complexes. PLoS ONE 11, e0146014, 1-21.CrossRefGoogle ScholarPubMed
Karimi, J., Hassani-Kakhki, M. and Awal, M.M. (2010) Identifying thrips (Insecta: Thysanoptera) using DNA Barcodes. Journal of Cell and Molecular Research 2, 35–41.Google Scholar
Katoh, K., Rozewicki, J. and Yamada, K.D. (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20, 1160–1166.CrossRefGoogle ScholarPubMed
Leão, E.U., Spadotti, D.M.A., Rocha, K.C.G., Lima, E.F.B., Tavella, L., Turina, M. and Krause-Sakate, R. (2017). Efficient detection of Frankliniella schultzei (Thysanoptera, Thripidae) by cytochrome oxidase I gene (mtCOI) direct sequencing and real-time PCR. Brazilian Archives of Biology and Technology 60, e17160425.Google Scholar
Lis, J.A., Lis, B. and Ziaja, D.J. (2016) In BOLD we trust? A commentary on the reliability of specimen identification for DNA Barcoding: a case study on burrower bugs (Hemiptera: Heteroptera: Cydnidae). Zootaxa 4114, 83–86.CrossRefGoogle Scholar
Marullo, R., Mercati, F. and Vono, G. (2020) DNA Barcoding: a reliable method for the identification of thrips species (Thysanoptera, Thripidae) collected on sticky traps in onion fields. Insects 11, 1–10.CrossRefGoogle ScholarPubMed
Meiklejohn, K.A., Damaso, N. and Robertson, J.M. (2019) Assessment of BOLD and GenBank – their accuracy and reliability for the identification of biological materials. PLoS ONE 14, e0217084.CrossRefGoogle ScholarPubMed
Mound, LA and Palmer, JM (1981) Identification, distribution and host-plants of the pest species of Scirtothrips (Thysanoptera: Thripidae). Bulletin of Entomological Research 71, 467–479.CrossRefGoogle Scholar
Mutanen, M., Kivelä, S.M., Vos, R.A., Doorenweerd, C., Ratnasingham, S., Hausmann, A., Huemer, P., Dincă, V., van Nieukerken, E.J., Lopez-Vaamonde, C., Vila, R., Aarvik, L., Decaëns, T., Efetov, K.A., Hebert, P.D.N., Johnsen, A., Karsholt, O., Pentinsaari, M., Rougerie, R., Segerer, A., Tarmann, G., Zahiri, R. and Godfray, H.C.J. (2016) Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera. Systematic Biology 65, 1024–1040.CrossRefGoogle ScholarPubMed
Paradis, E. and Schliep, K. (2019) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics (Oxford, England) 35, 526–528.Google ScholarPubMed
Pentinsaari, M., Ratnasingham, S., Miller, S.E. and Hebert, P.D.N. (2020) BOLD and GenBank revisited – Do identification errors arise in the lab or in the sequence libraries? PLoS ONE 15, e0231814.CrossRefGoogle ScholarPubMed
Ratnasingham, S. and Hebert, P.D.N. (2007) BOLD: the barcode of life data system (www.barcodinglife.org). Molecular Ecology Notes 7, 355–364.CrossRefGoogle ScholarPubMed
Ratnasingham, S and Hebert, PDN (2013) A DNA-based registry for all animal species: the barcode index number (BIN) system. PLoS ONE 8, e66213.CrossRefGoogle ScholarPubMed
Rebijith, KB, Asokan, R, Krishna, V, Ranjitha, HH, Krishna Kumar, NK and Ramamurthy, VV (2014) DNA Barcoding and elucidation of cryptic diversity in thrips (Thysanoptera). Florida Entomologist 97, 1328–1347.CrossRefGoogle Scholar
Rugman-Jones, P.F., Hoddle, M.S. and Stouthamer, R. (2010) Nuclear-mitochondrial barcoding exposes the global pest Western flower thrips (Thysanoptera: Thripidae) as two sympatric cryptic species in its native California. Journal of Economic Entomology 103, 877–886.CrossRefGoogle ScholarPubMed
Sonet, G., Jordaens, K., Braet, Y., Bourguignon, L., Dupont, E., Backeljau, T., De Meyer, M. and Desmyter, S. (2013) Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France. Zookeys 365, 307–328.CrossRefGoogle Scholar
Srivathsan, A. and Meier, R. (2012) On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 28, 190–194.CrossRefGoogle ScholarPubMed
Struck, T.H. and Cerca De Oliveira, J. (2019) Cryptic species and their evolutionary significance. Encyclopedia of Life Sciences, 1–9. https://doi.org/10.1002/9780470015902.a0028292Google Scholar
Struck, T.H., Feder, J.L., Bendiksby, M., Birkeland, S., Cerca, J., Gusarov, V.I. and …Dimitrov, D. (2018). Finding evolutionary processes hidden in cryptic species. Trends in Ecology & Evolution, 33, 153–163.CrossRefGoogle ScholarPubMed
ThripsWiki (2023) ThripsWiki - providing information on the World's thrips. Available from: http://thrips.info/wiki/Main_Page (Accessed May 2023).Google Scholar
Timm, V.F., Gonçalves, L.T., Valente, V.L.D.S. and Deprá, M. (2022) The efficiency of the COI gene as a DNA Barcode and an overview of Orthoptera (Caelifera and Ensifera) sequences in the BOLD System. Canadian Journal of Zoology 100, 710–718.CrossRefGoogle Scholar
Tyagi, K., Kumar, V., Singha, D., Chandra, K., Laskar, B.A., Kundu, S., Chakraborty, R. and Chatterjee, S. (2017) DNA Barcoding studies on thrips in India: Cryptic species and species complexes. Scientific Reports 7, 1–14.CrossRefGoogle ScholarPubMed
Vink, C.J, Paquin, P. and Cruickshank, R.H. (2012) Taxonomy and irreproducible biological science. BioScience 62, 451–452.Google Scholar
Xiao, J.H., Wang, N.X., Murphy, R.W., Cook, J., Jia, L.Y. and Huang, D.W. (2012) Wolbachia infection and dramatic intraspecific mitochondrial DNA divergence in a fig wasp. Evolution 66, 1907–1916.CrossRefGoogle Scholar
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