DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing.
PacBio sequencing
allele polymorphism
intragenomic diversity
long-read high-throughput sequencing
paralogues
species identification
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Nov 2022
Nov 2022
Historique:
revised:
31
05
2022
received:
12
02
2022
accepted:
01
06
2022
pubmed:
7
6
2022
medline:
5
10
2022
entrez:
6
6
2022
Statut:
ppublish
Résumé
Molecular methods are increasingly used to identify species that lack conspicuous macro- or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long-read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population-level studies.
Identifiants
pubmed: 35666173
doi: 10.1111/1755-0998.13663
doi:
Substances chimiques
DNA, Fungal
0
RNA, Ribosomal, 28S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2871-2879Subventions
Organisme : Eesti Teadusfond
ID : PRG1170
Organisme : Eesti Teadusfond
ID : PRG632
Organisme : European Regional Development Fund
ID : Centre of Excellence EcolChange
Organisme : Estonian State Forest Management Centre
ID : Enhancing the conservation performance of protected forest fragments
Informations de copyright
© 2022 John Wiley & Sons Ltd.
Références
Anslan, S., & Tedersoo, L. (2015). Performance of cytochrome c oxidase subunit I (COI), ribosomal DNA large subunit (LSU) and internal transcribed spacer 2 (ITS2) in DNA barcoding of collembola. European Journal of Soil Biology, 69, 1-7.
Antich, A., Palacin, C., Wangensteen, O. S., & Turon, X. (2021). To denoise or to cluster, that is not the question: Optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics, 22, 1-24.
Bengtsson-Palme, J., Ryberg, M., Hartmann, M., Branco, S., Wang, Z., Godhe, A., De Wit, P., Sánchez-García, M., Ebersberger, I., de Sousa, F., Amend, A., Jumpponen, A., Unterseher, M., Kristiansson, E., Abarenkov, K., Bertrand, Y. J. K., Sanli, K., Eriksson, K. M., Vik, U., … Nilsson, R. H. (2013). Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution, 4, 914-919. https://doi.org/10.1111/2041-210X.12073
Bohmann, K., Mirarab, S., Bafna, V., & Gilbert, M. T. P. (2020). Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification. Molecular Ecology, 29, 2521-2534.
Byrne, A. Q., Rothstein, A. P., Poorten, T. J., Erens, J., Settles, M. L., & Rosenblum, E. B. (2017). Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis. Molecular Ecology Resources, 17, 1283-1292.
Callahan, B. J., Grinevich, D., Thakur, S., Balamotis, M. A., & Yehezkel, T. B. (2021). Ultra-accurate microbial amplicon sequencing with synthetic long reads. Microbiome, 9, 1-13.
Callahan, B. J., McMurdie, P. J., & Holmes, S. P. (2017). Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. The ISME Journal, 11, 2639-2643.
Coissac, E., Hollingsworth, P., Lavergne, S., & Taberlet, P. (2016). From barcodes to genomes: Extending the concept of DNA barcoding. Molecular Ecology, 25, 1423-1428.
Edgar, R. C. (2018). UNCROSS2: Identification of cross-talk in 16S rRNA OTU tables. BioRxiv, p.400762. https://doi.org/10.1101/400762
Estensmo, E. L., Maurice, S., Morgado, L., Martin-Sanchez, P. M., Skrede, I., & Kauserud, H. (2021). The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species. Molecular Ecology Resources, 21, 1141-1148.
Ganley, A. R., & Kobayashi, T. (2007). Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Research, 17, 184-191.
Gueidan, C., & Li, L. (2022). A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens. MycoKeys, 86, 195-212.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, 270, 313-321.
Hebert, P. D. N., Braukmann, T. W. A., Prosser, S. W. J., Ratnasingham, S., deWaard, J. R., Ivanova, N. V., Janzen, D. H., Hallwachs, W., Naik, S., Sones, J. E., & Zakharov, E. V. (2018). A sequel to Sanger: Amplicon sequencing that scales. BMC Genomics, 19, 1-14.
Hopple, J. S., & Vilgalys, R. (1994). Phylogenetic relationships among coprinoid txa and allies based on data from restriction site mapping of nuclear rDNA. Mycologia, 86, 96-107.
Hyde, K. D., Udayanga, D., Manamgoda, D. S., Tedersoo, L., Larsson, E., Abarenkov, K., Bertrand, Y., Oxelman, B., Hartmann, M., Kauserud, H., Ryberg, M., Kristiansson, E., & Nilsson, R. H. (2013). Incorporating molecular data in fungal systematics: A guide for aspiring researchers. Current Research in Environmental & Applied Mycology, 3, 1-32.
Karst, S. M., Ziels, R. M., Kirkegaard, R. H., Sørensen, E. A., McDonald, D., Zhu, Q., Knight, R., & Albertsen, M. (2021). High-accuracy long-read amplicon sequences using unique molecular identifiers with nanopore or PacBio sequencing. Nature Methods, 18, 165-169.
Katoh, K., Misawa, K., Kuma, K., & Miyata, T. (2002). MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059-3066.
Kolaříková, Z., Slavíková, R., Krüger, C., Krüger, M., & Kohout, P. (2021). PacBio sequencing of Glomeromycota rDNA: A novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi. The New Phytologist, 231, 490-499.
Kõljalg, U., Nilsson, R. H., Abarenkov, K., Tedersoo, L., Taylor, A. F., Bahram, M., Bates, S. T., Bruns, T. D., Bengtsson-Palme, J., Callaghan, T. M., & Douglas, B. (2013). Towards a unified paradigm for sequence-based identification of fungi. Molecular Ecology, 22, 5271-5277.
Li, Y., Yang, R. H., Jiang, L., Hu, X. D., Wu, Z. J., & Yao, Y. J. (2017). rRNA pseudogenes in filamentous ascomycetes as revealed by genome data. Genes, Genomes, Genetics, 7, 2695-2703.
Lindner, D. L., Carlsen, T., Nilsson, R. H., Davey, M., Schumacher, T., & Kauserud, H. (2013). Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi. Ecology and Evolution, 3, 1751-1764.
Lofgren, L. A., Uehling, J. K., Branco, S., Bruns, T. D., Martin, F., & Kennedy, P. G. (2019). Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles. Molecular Ecology, 28, 721-730.
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal, 17, 10-12.
Misas, E., Gómez, O., Botero, V., Muñoz, J., Teixeira, M., Gallo, J., Clay, O., & McEwen, J. (2020). Updates and comparative analysis of the mitochondrial genomes of Paracoccidioides spp. using Oxford nanopore MinION sequencing. Frontiers in Microbiology, 11, 1751.
Nilsson, R. H., Larsson, K.-H., Taylor, A. F. S., Bengtsson-Palme, J., Jeppesen, T. S., Schigel, D., Kennedy, P., Picard, K., Glöckner, F. O., Tedersoo, L., Saar, I., Kõljalg, U., & Abarenkov, K. (2018). The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47(D1), D259-D264.
Paloi, S., Mhuantong, W., Luangsa-Ard, J. J., & Kobmoo, N. (2021). Using high-throughput amplicon sequencing to evaluate intragenomic variation and accuracy in species identification of cordyceps species. Journal of Fungi, 7, 767.
Pawlowski, J., Audic, S., & Adl, S. (2012). CBOL protist working group: Barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biology, 10, e1001419.
Porter, T. M., & Hajibabaei, M. (2021). Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC Bioinformatics, 22, 1-20.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590-D596.
R Core Team (2020) R: A language and environment for statistical computing. : R Foundation for Statistical Computing. https://www.R-project.org/ Accessed 31 October 2021.
Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016). VSEARCH: A versatile open source tool for metagenomics. PeerJ, 4, e2584.
Sahlin, K., Lim, M. C., & Prost, S. (2021). NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data. Ecology and Evolution, 11, 1392-1398.
Sandin, M. M., Romac, S., & Not, F. (2021). Intra-genomic rDNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing. bioRxiv, 2021, 463214.
Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences USA, 74, 5463-5467.
Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One, 11, e0163962. https://doi.org/10.1371/journal.pone.0163962
Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., Chen, W., Bolchacova, E., Voigt, K., Crous, P. W., Miller, A. N., Wingfield, M. J., Aime, M. C., An, K. D., Bai, F. Y., Barreto, R. W., Begerow, D., Bergeron, M. J., Blackwell, M., … Schindel, D. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proceedings of the National Academy of Sciences USA, 109, 6241-6246.
Simmons, D. R., Bonds, A. E., Castillo, B. T., Clemons, R. A., Glasco, A. D., Myers, J. M., Thapa, N., Letcher, P. M., Powell, M. J., Longcore, J. E., & James, T. Y. (2020). The zollection of zoosporic eufungi at the University of Michigan (CZEUM): Introducing a new repository of barcoded Chytridiomyceta and Blastocladiomycota cultures. IMA Fungus, 11, 1-22.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., & Weber, C. F. (2009). Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537-7541.
Srivathsan, A., Lee, L., Katoh, K., Hartop, E., Kutty, S. N., Wong, J., Yeo, D., & Meier, R. (2021). ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biology, 19, 1-21.
Taylor, J. W., & Swann, E. C. (1994). DNA from herbarium specimens. In B. Herrmann & S. Hummel (Eds.), Ancient DNA (pp. 166-181). Springer.
Thines, M., Crous, P. W., Aime, M. C., Aoki, T., Cai, L., Hyde, K. D., Miller, A. N., Zhang, N., & Stadler, M. (2018). Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus, 9, 177-183.
Tedersoo, L., Albertsen, M., Anslan, S., & Callahan, B. (2021). Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Applied and Environmental Microbiology, 87, e00626-21.
Tedersoo, L., & Anslan, S. (2019). Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences. Environmental Microbiology Reports, 11, 659-668.
Tedersoo, L., Bahram, M., Zinger, L., Nilsson, H., Kennedy, P., Yang, T., Anslan, S., & Mikryukov, V. (2022). Best practices in metabarcoding of fungi: from experimental design to results. Molecular Ecology, 31, 2769-2795.
Tedersoo, L., Liiv, I., Kivistik, P. A., Anslan, S., Kõljalg, U., & Bahram, M. (2016). Genomics and metagenomics technologies to recover ribosomal DNA and single-copy genes from old fruitbody and ectomycorrhiza specimens. MycoKeys, 13, 1-20.
Tedersoo, L., & Lindahl, B. (2016). Fungal identification biases in microbiome projects. Environmental Microbiology Reports, 8, 774-779.
Tedersoo, L., Suvi, T., Larsson, E., & Kõljalg, U. (2006). Diversity and community structure of ectomycorrhizal fungi in a wooded meadow. Mycological Research, 110, 734-748. https://doi.org/10.1016/j.mycres.2006.04.00
Vu, D., Groenewald, M., De Vries, M., Gehrmann, T., Stielow, B., Eberhardt, U., Al-Hatmi, A., Groenewald, J. Z., Cardinali, G., Houbraken, J., & Boekhout, T. (2018). Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation. Studies in Mycology, 91, 23-36.
Wurzbacher, C., Larsson, E., Bengtsson-Palme, J., Van den Wyngaert, S., Svantesson, S., Kristiansson, E., Kagami, M., & Nilsson, R. H. (2019). Introducing ribosomal tandem repeat barcoding for fungi. Molecular Ecology Resources, 19, 118-127.