Characterization and identification of agarwood-producing plants (Aquilaria spp.) from North Aceh, Indonesia, based on morphological and molecular markers




Abstract. Lukman, Dinarti D, Siregar UJ, Turjaman M, Sudarsono. 2022. Characterization and identification of agarwood-producing plants (Aquilaria spp.) from North Aceh, Indonesia, based on morphological and molecular markers. Biodiversitas 23: 4861-4871. Agarwood is one of the non-timber export commodities important as raw materials for bioindustry. There are 26 agarwood-producing plant species in Indonesia belonging to three families (Thymelaeaceae, Euphorbiaceae, and Fabaceae). This study aims to identify the agarwood-producing plant species in North Aceh District, Aceh Province, Indonesia, based on their morphological and molecular characters. The evaluated morphological characteristics include the bark and leaf structures of endemic plants. Molecular characterization was carried out by sequencing of matK, ITS, and trnL-trnF genes. The collected data were analyzed using the appropriate software, such as R software, BlastX, Geneious Prime and MEGA X. The evaluated 66 accessions were clustered into two major groups based on their morphology. Group 1 consisted of 10.61% of the evaluated accessions is identified as Aquilaria beccariana. Group 2 was further classified into two subclusters (Group 2a and 3b). Group 2a consisted of 10,61% of the accessions as A. malaccensis and Group 2b consisted of 78,79% of the accessions as A. microcarpa. All samples are identified as A. malaccensis based on the matK DNA sequences. Meanwhile, Groups 1 are identified as A. beccariana and Group 2a and 2b as A. microcarpa based on the ITS sequences. Based on the trnL-trnF sequences, Groups 1 and 2a was identified as A. malaccensis and Group 2b as A. microcarpa


Berjak P, Pammenter NW. 2013. Implications of the lack of desiccation tolerance in recalcitrant seeds. Front Plant Sci 4: 1-9. DOI: 10.3389/fpls.2013.00478.
Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). 2004. Amendments to Appendices I and II of CITES. In: Proceedings of the Thirteenth Meeting of the Conference of the Parties, Bangkok, Thailand.
Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). 2013. Iucn/Traffic Analyses of the Proposals to Amend the Cites Appendices at the 16th Meeting of the Conference of the Parties. CoP16 Inf. 14 (Rev. 1). Sixteenth Meeting of the Conference of the Parties Bangkok (Thailand), 3-14 March 2013.
Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B. 2013. Compressive genomics for protein databases. Bioinformatics 29: 1283-1290. DOI: 10.1093/bioinformatics/btt214.
Ellis B, Douglas CD, Leo JH, Kirk RJ, John DM, Peter W, Scott LW. 2009. Manual of Leaf Architecture. Cornell University Pr., United States of America.
Faizal A, Esyanti RR, Aulianisa AN, Iriawati, Santoso E, Turjaman M. 2017. Formation of agarwood from Aquilaria malaccensis in response to inoculation of local strains of Fusarium solani. Trees 31: 189-197. DOI: 10.1007/s00468-016-1471-9.
Gholibeigian M. 2021. CTAB –Extraction method in Plant tissue. 348693878.
Hariyati T, Kusnadi J, Arumingtyas EL. 2013. Genetic diversity of hybrid durian resulted from cross-breeding between Durio kutejensis and Durio zibethinus based on random amplified polymorphic DNAs (RAPDs). Am J Mol Biol 3: 153-157. DOI: 10.4236/ajmb.2013.33020.
Hartati RS, Sudarsono S. 2014. Inbreeding depression pada progeni hasil penyerbukan sendiri dan outbreeding depression pada hasil penyerbukan silang jarak pagar (Jatropha curcas L.). J Penelitian Tanaman Industri 20 (2): 65. DOI: 10.21082/jlittri.v20n2.2014.65-76. [Indonesian]
Hashim YZ, Kerr PG, Abbas P, Salleh MH. 2016. Aquilaria spp. (agarwood) as a source of health beneficial compounds: A review of traditional use, phytochemistry and pharmacology. J Ethnopharmacol 189: 331-360. DOI: 10.1016/j.jep.2016.06.055.
Hidayat A, Turjaman M, Qamyari R, Imanuddin R, Tohir D, Rahmanto RGH, Susilowati A. 2021. Bioactive composition, antifungal, antioxidant, and anticancer potential of essential agarwood oil from decaying logs (Gyrinops spp.) of Papua Island (Indonesia). JAPS 11 (10): 070-078. DOI: 10.7324/JAPS.
Hidayat H, Siburian R, Yuliana CI. 2020. Natural agarwood, trading networks and gaharu cultivation: Review on policy study in East Kalimantan. J Biologi Indonesia 16 (1): 99-110. DOI: 10.47349/jbi/16012020/99. [Indonesian]
Hou D. 1960. Thymelaeaceae. Flora Malesiana-Series 1, Spermatophyta 6: 1-48.
Hubert N, Hanner R. 2015. DNA Barcoding, species delineation and taxonomy: A historical perspective. Rev J De Gruyer 3: 44-58. DOI: 10.1515/dna-2015-0006.
Kalra R, Kaushik N. 2017. A review of chemistry, quality and analysis of infected agarwood tree (Aquilaria sp.). J Phytochem Rev 16 (4): 1-35. DOI: 10.1007/s11101-017-9518-0.
Kang Y. 2021. Molecular identification of Aquilaria species with distribution records in China using DNA barcode technology. Mitochondrial DNA Part B: Resour 6 (4): 1525-1535. DOI: 10.1080/23802359.2021.1914210.
Kementerian Lingkungan Hidup dan Kehutanan (KLHK). 2018. Kuota Pengambilan Tumbuhan Alam dan Penangkapan Satwa Liar. Periode Tahun 2018. KLHK SK.500/KSDAE/SET/KSA.2/12/2017. [Indonesian]
Kress WJ, Erickson DL. 2012. DNA barcodes: Methods and protocols, methods in molecular biology. Methods Mol Biol 858: 3-8. DOI: 10.1007/978-1-61779-591-6_1.
Kumar S, Stecher G, Tamura K. 2016. MEGA7. Molecular evolutionary genetic analysis version 7.0 for bigger datasets brief communication. Mol Biol Evol 33 (7): 170-174. DOI: 10.1093/bolbev/msw054.
Lee S, Mohamed R. 2016. Rediscovery of Aquilaria rostrata (Thymelaeaceae), a species thought to be extinct, and notes on Aquilaria conservation in Peninsular Malaysia. Blum - J Plant Tax and Plant Geog 61 (1): 13-19. DOI: 10.3767/000651916X691196.
Lee SY, Mohamed R, Faridah-Hanum I, Lamasudin DU. 2016b. Utilization of the internal transcribed spacer (ITS) DNA sequence to trace the geographical sources of Aquilaria malaccensis Lam. populations. Plant Genet Resour 16 (2): 103-111. DOI: 10.1017/S1479262117000016.
Lee SY, Ng WL, Mahat MN, Nazre M, Mohamed R. 2016a. DNA barcoding of the endangered Aquilaria (Thymelaeaceae) and its application in species authentication of agarwood products traded in the market. PLoS One 11 (4): e0154631. DOI: 10.1371/J.pone.0154631.
Lee SY, Turjaman M and Mohamed R. 2018. Phylogenetic relatedness of several agarwood-producing taxa (Thymelaeaceae) from Indonesia. Trop Life Sci Res 29 (2): 13-28. DOI: 10.21315/tlsr2018.29.2.2.
Lee SY, Turjaman M, Chaveerach A, Subasinghes SMCUP, Fan Q, Liao W. 2022. Phylogenetic relationships of Aquilaria and Gyrinops (Thymelaeaceae) revisited: Evidence from complete plastid genomes. Bot J Linn Soc 20: 1-16. DOI: 10.1093/botlinnean/boac014/6571443.
Li Q, Yan H, Lin D, Wang Y, He M, Zhang W, Gao X, Zhu S. 2018. Molecular identification of three Aquilaria (Thymelaeaceae) species through DNA barcoding. Biol Pharm Bull 41 (6): 967-971. DOI: 10.1248/bpb.b18-00050.
Li W, Cai CH, Guo ZK, Wang H, Zuo WJ, Dong WH, Mei WL, Dai HF. 2015. Five new eudesmane-type sesquiterpenoids from Chinese agarwood induced by artificial holing. Fitoterapia 100: 44-49. DOI: 10.1016/j.fitote.2014.11.010
Lim TK. 2015. Edible Medicinal and Non-medicinal Plants. Springer, Dordrecht. DOI: 10.1007/978-94-007-1764-0.
Liu Y, Chen H, Yang Y, Wei J, Meng H, Chen W, Feng J, Gan B, Chen X, Gao Z, Huang J, Chen B. 2017. Whole-tree agarwood inducing technique: An efficient novel technique for producing high-quality agarwood in cultivated Aquilaria sinensis trees. Molecules 18: 3086. DOI: 10.1016/S1674-6384(17)60072-8.
Nasution AA, Siregar UJ, Miftahudin, Turjaman M. 2019. Identification of chemical compounds in agarwood-producing species Aquilaria malaccensis and Gyrinops versteegii. J For Res 31: 1371-1380. DOI: 10.1007/s11676-018-00875-9.
Nguyen, Tra TH, Nguyen, Duy V. 2014. Biodiversity of major bacterial groups in association with agarwood (Aquilaria crassna) in Khanh Hoa Province, Vietnam. J Viet Environ 6 (2): 132-137. DOI: 10.13141/jve.vol6.no2.
Nugraha F, Roslim DI, Ardilla YP, Herman. 2014. Analysis of partial gene sequence ferritin2 on rice plants (Oryza sativa L.) Indragiri Hilir, Riau. Biosaintifika 6 (2): 70-79. DOI: 10.15294/biosaintifika.v6i2.3102.
Pammenter NW, Berjak P. 2014. Physiology of desiccation-sensitive (recalcitrant) seeds and the implications for cryopreservation. Intl J Plant Sci 175 (1): 21-28. DOI: 10.1086/673302.
Parker J, Helmstetter AJ, Devey D, Wikinson T, Papadopulos AST. 2017. Field-based species identification of closely-related plants using real-time nanopore sequencing. Sci Rep 7 (1): 8345. DOI: 10.1038/s41598-017-08461-5.
Rangkuti AB, Susilowati A, Siregar UJ, Irmayanti L, Siregar IZ. 2021. DNA barcoding of rattan (Arecaceae) from Gunung Walat Education Forest, Sukabumi-West Java. J Sylva Indones 4 (1): 45-53. DOI: 10.32734/jsi.v4i01.5563.
Roslim DI. 2019. Analysis of matK, rbcL and trnL-trnF Intergenic Spacer Sequences on Durik-Durik (Syzygium sp). J Phys Conf Ser 1351: 012023. DOI: 10.1088/1742-6596/1351/1/012023.
Santoso E. 2015. Valuasi Teknologi Gaharu Budidaya. Forda Press, Bogor. [Indonesian]
Siregar UJ, Maulana MI, Suharsono UW. 2017. Development of protocols for genomic library construction of Agarwood (Aquilaria malaccensis). Biodiversitas 18: 1150-1158. DOI: 10.13057/biodiv/d180336.
Songa B, Santiago MS, Moretob M, Johnsona Y, Bucklera ES, Stitzera MC. 2022. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. PNAS 119 1: e2113075119. DOI: 10.1073/pnas.2113075119.
Soomers H, Karssenberg D, Soons MB, Verweij PA Verhoeven JTA, Wassen MJ. 2013. Wind and water dispersal of wetland plants across fragmented landscapes. Ecosystems 16: 434-451. DOI: 10.1007/s10021-012-9619-y.
Suharti S. 2014. Peluang bisnis gaharu bersama masyarakat. In: Susmianto A, Turjaman M, Setio P (eds). Rekam Jejak: Gaharu Inokulasi, Teknologi Badan Litbang Kehutanan. Forda Press, Pusat Litbang Konservasi dan Rehabilitasi, Bogor. [Indonesian]
Susilo A, Kalima T, Santoso E. 2014. Panduan Lapangan Pengenalan Jenis Pohon Penghasil Gaharu Aquilaria spp. Di Indonesia. Pusat Penelitian dan Pengembangan Konservasi dan Rehabilitasi International Tropical Timber Organization (ITTO) – CITES Phase II Project. Bogor, Indonesia. [Indonesian]
Tallei TE, Kolondam BJ. 2015. DNA barcoding of sangihe nutmeg (Myristica fragrans) using matK Gene. Hayati 22 (1): 41-47. DOI: 10.4308/hjb.22.1.41.
Tan CS, Isa NM, Ismail I, Zainal Z. 2019. Agarwood induction: Current developments and future perspectives. REVIEW article. Front Plant Sci 10: 1-13. DOI: 10.3389/fpls.2019.00122
Tanaka S, Ito M. 2019. DNA barcoding for identification of agarwood source species using trnL-trnF and matK DNA sequences. J Nat Med 74 (2): 1-9. DOI: 10.1007/s11418-019-01338-z.
Tiana H, Wanga H, Yanga L, Gaia CJ, Donga WH, Lia W, Meia WL, Daia HF. 2019. Two new sesquiterpenoids from agarwood originated from Aquilaria sp. J Asian Nat Prod Res 22: 626-631. DOI: 10.1080/ 10286020.2019.160895.
Traveset A, Perez JRG. 2018. Seed dispersal. In: Jørgensen SE, Fath BD (eds). General Ecology. Vol. [4] of Encyclopedia of ecology, 5 vols. pp. [3188-3194] Elsevier, Oxford. DOI: 10.1016/B978-008045405-4.00860-0.
Turjaman M, Hidayat A. 2017. Agarwood-planted tree inventory in Indonesia. Earth Environ Sci 54: 012062. DOI: 10.1088/1755-1315/54/1/012062.
Wang L, Xie B, Shi J, Xue S, Deng Q, Wei Y, Tian B. 2010. Physicochemical properties and structure of starches from Chinese rice cultivars. Food Hydrocoll 24 (2-3): 208-216. DOI: 10.1016/j.foodhyd.2009.09.007.
Wang XY, Zheng SH, Liu Y, Han JP. 2016. ITS2, a better DNA barcode than ITS in identification of species in Artemisia L. Chinese Herb Med 8 (4): 352-358. DOI: 10.1016/S1674-6384(16)60062-X.
Wu SG, Forrest SB, Eric YX, Yu-Xuan W, Yi-Fan C, Qiao-Liang X. 2007. A leaf recognition algorithm for plant classification using probabilistic neural network. Signal Processing and Information Technology. Giza, Egypt, 15-18 December 2007. DOI: 10.1109/ISSPIT.2007.4458016.
Xue CY, Li DZ. 2011. Use of DNA barcode sensu lato to identify traditional Tibetan medicinal plant Gentianopsis paludosa. J Syst Evol 49 (3): 267-270. DOI: 10.1111/j.1759-6831.2011.00127.x.

Most read articles by the same author(s)

1 2 3 4 > >>