DNA barcoding of flowering plants in Sumatra, Indonesia

Amandita, Fitri Y.; Rembold, Katja; Vornam, Barbara; Rahayu, Sri; Siregar, Iskandar Z.; Kreft, Holger; Finkeldey, Reiner (2019). DNA barcoding of flowering plants in Sumatra, Indonesia. Ecology and evolution, 9(4), pp. 1858-1868. John Wiley & Sons, Inc. 10.1002/ece3.4875

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Abstract The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land-use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best-close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best-close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two-loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty-one species were found to be nonmonophyletic with both markers. The two-loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS) > Botanical Garden
08 Faculty of Science > Department of Biology > Institute of Plant Sciences (IPS)

UniBE Contributor:

Rembold, Katja

Subjects:

500 Science > 580 Plants (Botany)

ISSN:

2045-7758

Publisher:

John Wiley & Sons, Inc.

Language:

English

Submitter:

Peter Alfred von Ballmoos-Haas

Date Deposited:

11 Mar 2019 11:59

Last Modified:

24 Oct 2019 02:46

Publisher DOI:

10.1002/ece3.4875

PubMed ID:

30847077

Uncontrolled Keywords:

DNA marker, EFForTS project, matK, molecular identification, rbcL, Sumatra

BORIS DOI:

10.7892/boris.125801

URI:

https://boris.unibe.ch/id/eprint/125801

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