Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia
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MUHAMMAD FAUZI ARIF
https://orcid.org/0000-0001-9964-1294
GANIES RIZA ARISTYA
https://orcid.org/0000-0001-9251-5076
DYAH SUBOSITI
https://orcid.org/0000-0003-1596-5625
ANISKA NOVITA SARI
RINA SRI KASIAMDARI
♥
https://orcid.org/0000-0003-4125-1490
Abstract
Abstract. Arif MF, Aristya GR, Subositi D, Sai AN, Kasiamdari RS. 2019. Short Communication: rbcL and matK chloroplast DNA composition of green chireta (Andrographis paniculata) from Indonesia. Biodiversitas 20: 3575-3583. Green chireta (Andrographis paniculata (Burm.f.) Wall. ex Nees.) is often used by the traditional community as a medicinal herb in Indonesia. However, nucleotide study of green chireta from Indonesia has never been done. The objectives of this study were to analyze the rbcL and matK chloroplast gene composition of green chireta from Indonesia and to analyze the relationship with other Andrographis species. The result proved that all the DNA composition of green chireta used in this study was similar to the A. paniculata from GenBank. The rbcL composition was similar to A. paniculata KF521878, A. paniculata JQ922118, and A. paniculata JQ230990 from GenBank while the matK composition was similar to A. paniculata LC461762. Total 501 bp of rbcL and 639 bp of matK can be aligned produced 167 and 213 amino acid from translation. The amino acid translation result showed no different expression from rbcL genes but there was one sample expressed different translations from the matK gene. The phylogenetic tree was reconstructed using the Neighbor-Joining method with 1000 bootstrap values and the Kimura 2-Parameter (K2P) model in the MEGA7 software. Both rbcL and matK genes grouped the samples into the same clade as A. paniculata from GenBank. No variation was detected from the rbcL gene but two haplotypes were detected from the matK gene. This composition and sequence data serve as a database for Andrographis species from Indonesia which can be used for various studies.
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References
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Bafeel SO, Arif IA, Bakir MA, Khan HA, Farhan AH, Homaidan AA, Ahamed A, Thomas J. 2011. Comparative evaluation of PCR success with universal primers of maturase K (matK) and ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (rbcL) for barcoding of some arid plants. Plant Omics 4: 195e198.
CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 106: 12794-12797.
Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology 17: 134.
Ghorbani A, Saeedi Y, Boer HJ. 2017. Unidentifiable by morphology: DNA barcoding of plant material in local markets in Iran. PLoS ONE 12(4): e0175722.
Hilu KW, Liang H. 1997. The matK gene: sequence variation and application in plant systematics. American Journal of Botany 84: 830-839.
Hollingsworth PM, Graham SW, Little D P. 2011. Choosing and using a plant DNA barcode. PLoS ONE 6: e19254
Joselin J, Jeeva S. 2014. Andrographis paniculata: A review of its traditional uses, phytochemistry and pharmacology. Medicinal & Aromatic Plants 3(4): 1-15.
Librado P, Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33(7): 1870-1874.
Kool A, Boer HJ, Krüger A, Rydberg A, Abbad A, Björk L, Martin G. 2012. Molecular identification of commercialized medicinal plants in Southern Morocco. PLoS ONE 7: e39459.
Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 2: 8369-8374.
Kumar V, Thakur AK, Chatterjee SS. 2014. Perspective of Andrographis paniculata in neurological disorders. Clinical Pharmacology & Biopharmaceutics S2: 5-8.
Li DZ, Gao LM, Li HT. 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences of the United States of America 108: 19641-19646.
Maddison WP, Maddison DR. 2017. Mesquite: a modular system for evolutionary analysis. Ver 3.31. http://mesquiteproject.org.
Mulyati R, Setyowati FM. 1996. Sambiloto’s ethnobotany, its use as an ingredient of traditional medicine. Warta Tumbuhan Obat Indonesia 3: 29. [Indonesian]
Ministry of Trade Republic of Indonesia. 2009. Indonesian Herbal: The Tradisional Therapy. Trade Research and Development Agency Ministry of Trade, Jakarta.
Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
Neves SS, Forrest LL. 2011. Plant DNA sequencing for phylogenetic analyses: from plants to sequences. Methods in Molecular Biology 781:183-235.
Newmaster SG, Fazekas AJ, Ragupathy S. 2006. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany 84: 335-341.
Pujiasmanto B, Moenandir J, Syamsulbahri, Kuswanto. 2007. Agroecological and morphological studies of bitter (Andrographis paniculata Nees.) In various habitats. 8(4): 326-329. [Indonesian]
Saitou N, Nei M. 1987. The Neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4): 406-425.
Sass C, Little DP, Stevenson DW, Specht CD. 2007. DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS ONE 2: e1154.
Smith SA, Donoghue MJ. 2008. Rates of molecular evolution are linked to life history in flowering plants. Science 322: 86-89.
Wahyono. 2017. National Report on Exploration of Local Knowledge of Ethnomedicine and Community-Based Medicinal Plants in Indonesia. Ministry of Health Republic of Indonesia B2P2TOOT, Tawangmangu. [Indonesian]
von Rintelen K, Arida E, Häuser C. 2017. A review of biodiversity-related issues and challenges in megadiverse Indonesia and other Southeast Asian countries. Research Ideas and Outcomes 3: 1-6.
Yu J, Xue JH, Zhou SL. 2011. New universal matK primers for DNA barcoding angiosperms. Journal of Systematics and Evolution 49: 176e181
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