Abstract
Difficulties in identifying Vanda species are still encountered, and the ambiguity in its taxonomy is still unresolved. To date, the advancement in molecular genetics technology has given rise to the molecular method for plant identification and elucidation. One hundred twenty-five (125) gene sequences of Vanda species from the Philippines were obtained from the NCBI GenBank. Four of the 25 loci were further examined using MEGA 11 software for multiple sequence alignment, sequence analysis, and phylogenetic reconstruction. The indel-based and tree-based methods were combined to compute the species resolution. The result showed that ITS from the nuclear region obtained the highest species resolution with 66.67%. It was then followed by psbA-trnH, matK, and trnL-trnF from the chloroplast genome with a species resolution of 60%, 40%, and 30.77%, respectively. ITS and psbA-trnH satisfied the ideal length for DNA barcoding as they have 655 bp and 701 bp, respectively. The locus psbA-trnH was also considered to have a higher potential to discriminate Vanda species since only a few sequences were tested for ITS. Furthermore, ITS and trnL-trnF have the highest variable rate, which is 2.9%, while matK and psbA-trnH have 2% and 1.3%, respectively. This showed the nature of the unique sequences of various species. In this study, the indel-based method provided better results than the tree-based method. It will help support further DNA barcoding studies and strengthen the conservation and protection of Vanda spp. in the Philippines.
Publisher
W. Szafer Institute of Botany Polish Academy of Sciences
Subject
Plant Science,General Medicine
Reference21 articles.
1. Chatzou, M., Magis, C., Chang, J. M., Kemena, C., Bussotti, G., Erb, I. & Notredame, C. 2016. Multiple sequence alignment modeling: methods and applications. Briefings in Bioinformatics 17(6): 1009-1023. https://doi.org/10.1093/bib/bbv099
2. DENR Administrative Order 2017. Updated national list of threatened Philippine plants and their categories. (DAO 2017-11). https://bmb.gov.ph/index.php/facts-and-figures-wild/national-list-of-threatened-flora. Access date: February 2022.
3. Dizon, S. A., Ocenar, A. P. & Naïve, M. A. K. 2018. Inventory of orchids in the Mount Hamiguitan Range Wildlife Sanctuary, Davao Oriental, Philippines. Bio Bulletin 4(1): 37-42.
4. Edgar, R. C. 2004a. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. https://doi.org/10.1093/nar/gkh340
5. Edgar, R. C. 2004b. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC bioinformatics 5: 113.