Shorea is a genus of tropical hardwood trees found throughout Southeast Asia. All species of Shorea form symbiotic root associations with ectomycorrhizal fungi (ECM). At Lambir Hills National Park in Malaysian Borneo, there are over 50 different species of Shorea, many with overlapping distributions. This means that any root core samples used to study ECM assembly will contain a mix of ECM roots from many different host trees. I am interested in characterizing differences between the ECM communities associated with three species of Shorea; S. acuta, S. almon and S. inappendiculata (fig. 1). In order to ensure that the ECM root samples collected in the vicinity of these target trees are actually associated with them, I need to develop a DNA barcode that can distinguish between species of Shorea.
Figure 2-PCR amplification results from primers designed for ITS1 (A) and ITS2 (B). Amplicons were loaded on a 1% agarose gel. Specimens of each species of Shorea are labeled 1-3, NC denotes no template, negative control.
Figure 3-Sections of ITS1 (A) and ITS2 (B) alignments showing base pair changes and insertion/deletions that differentiate between S. inappendiculata and S. almon/S. acuta
Figure 4-Pairwise similarity (%) of S. acuta and S. almon ITS1 sequences
Shorea is a genus of tropical hardwood trees found throughout Southeast Asia. The purpose of this study was to develop a DNA barcode for three species of Shorea found in Malaysian Borneo: S. acuta, S. almon and S. inappendiculata. In order to distinguish between these three species, primers were designed to target internal transcribed spacers (ITS) 1 and 2, two non-functional regions of ribosomal DNA. ITS1 and ITS2 were successfully amplified and sequenced for each species. Both loci contained variation that could identify S. inappendiculata, but neither were able to distinguish between S. acuta and S. almon. An additional barcoding locus is necessary in order to genetically identify these species
Chen, Shilin, H. Yao, J. Han, C. Liu, J. Song, L. Shi, Y. Zhu, X. Ma, T. Gao, X. Pang, K. Luo, Y. Li, X. Li, X. Jia, Y. Lin, C. Leon. 2010. “Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plants. PLoS ONE 5(1): e8613.
Kamiya, Koichi, Y. Gan, S. Lum, M. S. Khoo, S. C. Chua, N. Faizu. 2011. Morphological and molecular evidence of natural hybridization in Shorea. Tree Genetics & Genomes, 7(2): 297-306.
Dr. Krista McGuire provided the impetus and direction for this project. Dr. Kabir Peay was extremely helpful negotiating my permission to conduct research at Lambir Hills National Park. I would like to thank Dr. Stuart Davies for providing tree distribution data for Lambir Hills, and Krystal Diaz and Amos Lim for giving me so much help in the field. Catharina Grubaugh and Kate Reid deserve a medal for their endless patience throughout this project and beyond. I would also like to thank Dr. Berish Rubin for his valuable guidance and constant support
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