Abstract
Given the difficulties for rapid biodiversity assessments in understudied regions, DNA barcoding appears as a suitable alternative. Still, this approach relies heavily on accurate reference sequence databases for correct taxonomic assignments. In this study, we evaluated the effectiveness of matK, rbcL, and ITS regions for the identification of Myrtaceae species with emphasis on the megadiverse genus Syzygium from Sumatra, Indonesia; and analyzed the applicability of species-tree inference for species assignment using barcode markers. ITS was the most variable barcode region (42.6% of variable sites), followed by matK (25.7%), and rbcL (14.9%). In terms of assignments of sequences using the BLAST algorithm, all markers were effective for genus-level attribution. For assignments at species rank, rbcL was able to attribute 30.15% of the samples at the species level, followed by matK (26.47%), and ITS (17.21%). These results are largely related to the availability of reference sequences for Myrtaceae in the databases since for the 27 species analyzed in this study, only 8 species had reference sequences for all three barcode regions available in GenBank. The species-tree inference based on the combination of matK, rbcL, and ITS markers recovered 41% of the species as monophyletic clades with strong node support. Due to its high level of differentiation, we recommend the ITS region as the most efficient barcode marker for the identification of Syzygium, and the traditional core-barcodes (matK + rbcL) as add-on barcodes.
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22 July 2022
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Acknowledgements
We thank Katja Rembold and the EFForTS B06/B14 field and herbarium teams for sampling and management of Myrtaceae specimens. Furthermore, we acknowledge our technicians Gudrun Diederich, Larissa Kunz, and Oleksandra Dolynska for their assistance with DNA isolation, amplification, and sequencing. Moreover, we appreciate the Ministry of Research and, Technology (RISTEK)/Agency for Research and Innovation (BRIN) of the Republic of Indonesia (RISTEKDIKTI) for permitting us to perform the research in Indonesia, and recognize the support of the German Research Foundation. We thank the two anonymous reviewers for contributing with valuable comments to our manuscript.
Funding
This research was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) as part of the EFForTS project (Collaborative Research Centre 990, https://www.uni-goettingen.de/efforts), project number 192626868.
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Development of concept, all authors; Sampling preparation and specimen processing, F.Y.A., I.Z.S, C.C.M.M. and F.B; Bioinformatics analysis, R.W., F.Y.A., and C.C.M.M.; Data curation, R.W., F.Y.A., C.C.M.M. and F.B.; Original draft preparation, R.W. and C.C.M.M.; Review and editing, all authors.
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Data Archiving Statement
All sequences used in this study have been submitted to GenBank (NCBI), accession numbers are MT864746 to MW854235 (details in Table S1).
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Communicated by G.G. Vendramin
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Wati, R., Amandita, F.Y., Brambach, F. et al. Filling gaps of reference DNA barcodes in Syzygium from rainforest fragments in Sumatra. Tree Genetics & Genomes 18, 6 (2022). https://doi.org/10.1007/s11295-022-01536-z
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DOI: https://doi.org/10.1007/s11295-022-01536-z