Filling gaps of reference DNA barcodes in Syzygium from rainforest fragments in Sumatra

Springer Science and Business Media LLC - Tập 18 - Trang 1-15 - 2022
Ridha Wati1,2, Fitri Yola Amandita3, Fabian Brambach4, Iskandar Z. Siregar2,5, Oliver Gailing6,7, Carina Carneiro de Melo Moura7
1Tropical Silviculture Study Program, Graduate School of IPB University (Bogor Agricultural University), Bogor, Indonesia
2Department of Silviculture, Faculty of Forestry and Environment, IPB University (Bogor Agricultural University), Bogor, Indonesia
3Center for Research and Development of Environmental Quality and Laboratory, Ministry of Environment and Forestry of Indonesia, South Tangerang, Indonesia
4Biodiversity, Macroecology and Biogeography, University of Göttingen, Göttingen, Germany
5Advanced Research Laboratory (ArLab), IPB University (Bogor Agricultural University), Bogor, Indonesia
6Centre of Biodiversity and Sustainable Land Use, University of Göttingen, Göttingen, Germany
7Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, Göttingen, Germany

Tóm tắt

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.

Tài liệu tham khảo

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