Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene

##plugins.themes.bootstrap3.article.sidebar##

PDF
DOI https://doi.org/10.13057/biodiv/d220934
Issue
Vol. 22 No. 9 (2021)
Section
Articles

##plugins.themes.bootstrap3.article.main##

SUJIT SIL ♥
Department of Botany, Hooghly Muhammad Mohsin College. Chinsurah, Hooghly, PIN- 712101, W.B., India
https://orcid.org/0000-0002-8426-960X
KALYAN KUMAR DE
Department of Botany, Hooghly Muhammad Mohsin College. Chinsurah, Hooghly, PIN- 712101, W.B., India
ASOK GHOSH
Taxonomy of Angiosperms and Biosystematics Section, UGC-CAS Department of Botany, The University of Burdwan. Golapbag, Burdwan, PIN-713104, W.B., India

Abstract

Abstract. Sil S, De KK, Ghosh A. 2021. Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene. Biodiversitas 22: 3880-3889. Saraca L. is one of the most important genera, with several horticultural and therapeutic values. Specific taxonomic and phylogenetic knowledge of Saraca through molecular data is essential for accessing its true medicinal benefits. Nineteen different Partial matK gene sequences of the chloroplast genome of six different species of Saraca, including four amplified and 15 retrieved from the NCBI gene bank, were place in a sequence alignment. The resulting data were examined to determine their phylogenetic and evolutionary interrelationships. The comparative analysis of different sequences of each of the species revealed intra-specific molecular diversity, and the comparison of the matK sequences of six different species defined their inter-specific molecular diversity. The analysis of partial matK sequences revealed the presence of 87 variable sites, 14 parsimony informative sites, 54 singleton sites, and 237 quadri-fold degenerate sites. The approximate nucleotide composition was A-31.02%, T-37.46%, C-16.06%, and G-15.46%. The value of transition/transversion bias was 0.90. About 522 codons were analyzed and the presence of 34 variable sites, 8 parsimony informative sites, and 25 singleton sites was observed within their respective amino acid sequences. The average pair-wise distance was 0.0444, and 189 segregating sites and 0.018809 nucleotide diversity were observed. The evolution of different species of Saraca and their phylogenetic interrelationships were observed by analyzing their matK sequences. The relative homogeneity of S. indica is quite low. S. dives had the earliest evolutionary trends while S. declinata had the most recent. S. asoca and S. indica are quite similar on the molecular level but can be treated as different species while the difference between S. declinata and one of its synonyms, S. palembanica, indicates the possibility of separating them into different species.

##plugins.themes.bootstrap3.article.details##

References
Banks H, Klitgaard B. 2000. Palynological contribution to the systematics of detarioid legumes. In: Herendeen PS, Bruneau A (eds.) Advances in legume systematics. Royal Botanic Gardens, Kew.
Begum SN, Ravikumar K, Ved DK. 2014. ‘Asoka’- an important medicinal plant, its market scenario and conservation measures in India. Curr Sci 107(1): 26-28.
CAMP Workshops on Medicinal Plants, India. 1998. Saraca asoca. The IUCN Red List of Threatened Species 1998: e.T34623A9879360.
Estrella MDL, Forest F, Wieringa JJ, Fougère-Danezan M, Bruneau A. 2017. Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees. New Phytol 214: 1722–1735, DOI: https://doi.org/10.1111/nph.14523
Estrella MDL, Forest F, Klitgard B, Lewis GP, Mackinder BA, Queiroz LPD, Wieringa JJ, Bruneau A. 2018. A new phylogeny-based tribal classification of subfamily Detarioideae, an early branching clade of florally diverse tropical arborescent legumes. Sci Rep 8:6884. DOI:10.1038/s41598-018-24687-3
Gao T, Sun Z, Yao H, Song J. 2011. Identification of Fabaceae plants using the DNA barcode matK. Planta Med 77(1): 92-96. DOI: https://doi.org/10.1055/s-0030-1250050
Gogoi B, Bahu BS. 2018. DNA barcoding of the genus Nepanthes (Pitcher plant): a preliminary assessment towards its identification. BMC Plant Bio 18:153. DOI: https://doi.org/10.1186/s12870-018-1375-5
Guzman B, Vargas P. 2009. Historical biogeography and character evolution of Cistaceae (Malvales) based on analysis of plastid rbcL and trnL-trnF sequences. Organisms Diversity Evol 9: 83-99. DOI: https://doi.org/10.1016/j.ode.2009.01.001
Hegde S, Saini A, Hegde HV, Kholkute SD, Roy S. 2018. Molecular identification of Saraca asoca from its substituents and adulterants. 3 Biotech 8:161. DOI: https://doi.org/10.1007/s13205-018-1175-5
Hou D, Larsen K, Larsen SS. 1996. Cesalpiniaceae. In: Kalkman C et al. (eds.) Flora Malesiana. vol. 12, pp. 660-673. Rijksherbarium/Hortus Botanicus, Leiden.
Ito M, Kawamoto A, Kita Y, Yukawa T, Kurita S. 1999. Phylogenetic relationships of Amaryllidaceae based on matK sequence data. J Plant Res 112: 207–216
Jayakumar G, Ajithabai MD, Sreedevi S, Viswanathan PK, Remeshkumar B, 2010. Ethnobotanical survey of the plants used in the treatment of diabetes. Indian J Tradit knowl 9: 100-104.
Johnson LA, Soltis DE. 1994. matK DNA sequence and phylogenetic reconstruction in Saxifragaceae. Syst Bot 19: 143–156.
Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In: Munro HN (ed.). Mammalian protein metabolism. Acad Press New York.
Kim DK, Kim JH. 2011. Molecular phylogeny of tribe Forsythieae (Oleaceae) based on nuclear ribosomal DNA internal transcribed spacers and plastid DNA trnL-F and matK gene sequences. J Plant Res 124: 339–347. DOI: https://doi.org/10.1007/s10265-010-0383-9
Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: ll l-120.
Kirtikar, K.R., Basu, B.D., 1975. Indian medicinal plant. International book distributors, Dehradun.
Kress WJ. 2017. Plant Dna barcodes: Applications today and in the future. J Syst Evol 55(4): 291-307. DOI: https://doi.org/10.1111/jse.12254
Kumar S, Gadagkar SR. 2001. Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158: 1321–1327
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Bio Evo 35: 1547-1549.
Lahaye R, Bank MVD, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG., Savolainen V. 2007. DNA barcoding the floras of biodiversity hotspots. Proceed Nat Aca Sci United State Amer 105(8): 2923-2828. DOI: https://doi.org/10.1073/pnas.0709936105
Li Y, Gao LM, Poudel RC, Li DZ, Forrest A. 2011. High universality of matK primers for barcoding gymnosperms. J Syst Evol 49(3): 169-175. DOI: https://doi.org/10.1111/j.1759-6831.2011.00128.x
Lis JT. 1980. Fractionation of DNA fragments by polyethylene glycol induced precipitation. Methods in Enzymol 65: 347-353. DOI: https://doi.org/10.1016/S0076-6879(80)65044-7
Lledo MD, Davis AP, Crespo MB, Chase MW, Fay MF. 2004. Phylogenetic analysis of Leucojum and Galanthus (Amaryllidaceae) based on plastid matK and nuclear ribosomal spacer (ITS) DNA sequences and morphology. Plant Syst and Evol 246:223-243
LPWG. 2017. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon, 66: 44–77.
Lu JM, Wen J, Lutz S, Wang YP, Li DZ. 2012. Phylogenetic relationships of Chinese Adiantum based on five plastid markers. J Plant Res 125: 237–249. doi: https://doi.org/10.1007/s10265-011-0441-y
Mishra SB, Vijaykumar M. 2014. Anti-hyperglycemic and anti-oxidant effect of Saraca asoca (Roxb. De Wilde) flowers in Streptozotocin-Nicotinamide induced diabatic rat: A therapeutic stydy. J Bioanal Biomed 2: 338-343. DOI: https://doi.org/10.4172/1948-593X.S12-003
Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, Sundaresan V. 2015. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnol J 14(1): 8-21. DOI: https://doi.org/10.1111/pbi.12419
Miquel FAG. 1860. Flora van Nederlandsch Indie. Lipsiae apud Frid. Fleischer. Mdccclv.
Mohan C, Reddy MS, Kumar SM, Manzelat SF, Cherku PD. 2017. RAPD studies of Saraca asoca by fluorescent-labeled primers and development of micropropagation protocol for its conservation. Int J appl Agri Res 12(2): 137-151.
Monkheang P, Runglawan S, Tanee T, Noikotr K. 2011. Species diversity, usages, molecular markers and barcode of medicinal Senna species (Fabaceae, Caesalpinioideae) in Thailand. J Med Plant Res 5(26): 6173-6181. DOI: https://doi.org/10.5897/JMPR11.1075
More RP, Chandrashekhar M, Purohit HJ. 2016. matK-QR classifier: a patterns based approach for plant species identification. BioData Mining 9: 39. DOI: https://doi.org/10.1186/s13040-016-0120-6
Nag D, Ghosh M, Mukherjee A. 2013. Antimutagenic and genoprotective effects of Saraca asoca bark extract. Toxicol Ind Health 1: 1-8.
Nei M, and Kumar S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
Neuhaus H, Link G. 1987. The chloroplast tRNALys (UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide. Current Genetics. 11: 251-257
Nguyen TP, Trang NM, Due NM, Sinh NV, Triest L. 2015. Application of DNA barcoding markers to the identification of Hopea species. Genetics Mol. Res. 14(3): 9181-9190. DOI: https://doi.org/10.4238/2015.August.7.28
Nooten MBHV. 1880. Fleurs Fruits et Feuillages choisis de L’ile de Java. Librairie Europeenne C. Muquardt. Bruxelles.
Pagel M. 1999. Inferring the historical pattern of biological evolution. Nature 401: 877–884.
Pal TK, Bhattacharya S, Dey A. 2014. Evaluation of antioxidant activities of flower extract (Fresh and dried) of Saraca indica grown in West Bengal. Int J Current Microb Appl Sci 3(4): 251-259.
Pierre L. 1895. Flore Forestiere de la Cochinchine. Doin. Paris.
Pradhan P, Joseph L, Gupta V, Chulet R, Arya H. 2009. Saraca asoca (Ashoka): a review. J Chem Pharma Res 1: 62-71.
Prain D. 1897. The Journal of the Asiatic Society of Bengal. Bishop’s Collage Press. Calcutta.
Preeti B, Bharti A, Sharma AN, Singh V. 2012. A review on Saraca indica plant. Int Res J Pharma 3: 80-84.
Reddy BU. 2009. A phylogenetic analysis of the Cucurbitaceae: evidences from matK nucleotide sequences. Int J Bioinformatics Res 1(2): 47–53
Roxburgh W. 1799. A description of the Jonesia. Asia Res 4: 368-371.
Khan SZ, Ashfaq M, Ullah S. 2016. Evaluation of the discriminatory power of plant DNA barcodes rbcl and matK between species of Fabaceae. Int J Biosci 8(5): 75-86.
Saha J, Mitra T, Gupta K, Mukherjee S. 2012. Phytoconstituents and HPTLC analysis in Saraca asoca (roxb.)Wilde. Int J Pharm Sci 4(l): 96–99.
Saha J, Gupta K, Gupta B. 2013. Phylogenetic analyses and evolutionary relationships of Saraca asoca with their allied taxa (Tribe-Detarieae) based on the chloroplast matK gene. J. Plant Biochem. Biotechnol. DOI: https://doi.org/10.1007/s13562-013-0237-3
Saini A, Hegde S, Hegde HV, Kholkute SD, Roy S. 2018. Assessment of genetic diversity of Saraca asoca (Roxb.) De Wilde: a commercially important, but endangered, forest tree species in Western Ghats, India. New Zealand J of Forestry Sci 48:17. DOI: https://doi.org/10.1186/s40490-018-0122-x
Sanjappa M. 1992. Legumes of India. B. Sing and M. Pal Singh Publication, Dehradun.
Santapau H, Henry AN, 1973. Dictionary of flowering plants of India. New Delhi Publication and Information Directorate, New Delhi.
Scotland RW, Olmstead RG, Bennett JR. 2003. Phylogeny reconstruction: the role of morphology. Syst Biol 52: 539–548.
Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL. 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92: 142-166.
Sherin, D.R., Manojkumar, T.K. 2017. Flavonoids from Saraca asoca- Ideal medication for breast cancer: A molecular simulation approach. 1(6):1-3. DOI: 10.26717/BJSTR.2017.01.000533
Sil S, Mallick T, De KK, Pramanik A, Ghosh A. 2018. Comparative morphological study of three species of Saraca L. (Fabaceae) by the statistical approach to find out the logic of potent morphological markers. Beni-Suef Univ J Basic Appl Sci 7: 612-619.
Sil S, Mallick T, Pal T, Mondal A, De K.K, Ghosh A. 2019. Pollen morphology of Indian species of Saraca L. (Leguminosae)- A threatened and legendary medicinal tree. Phyton 88(3): 295-315. DOI: https://doi.org/10.32604/phyton.2019.06907
Tajima F, Nei M. 1984. Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1: 269-285.
Tajima F. 1989. Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
Takahata N, Kimura M. 1981. A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes. Genetics 98: 641-657.
Tamura K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol Biol Evol 9: 678-687.
Tamura K. Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526.
Thiers B. 2019. [continuously updated] Index Herbariorum: A global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium. http://sweetgum.nybg.org/science/ih/ (accessed on 25th March 2019).
Torres DC, Lima JPMS, Fernandes AG, Nunes EP, Grangeiro TB. 2011. Phylogenetic relationships within Chamaecrista sect. Xerocalyx (Leguminosae, Caesalpinioideae) inferred from the cpDNA trnE-trnT intergenic spacer and nrDNA ITS sequences. Genetics Mol Biol 34: 244-251.
Tucker SC. 2000. Floral development and Homeosis in Saraca (Leguminosae: Caesalpinioideae: Detarieae). Int J Plant Sci 161: 537-549.
Vijayan K, Tsou CH. 2010. DNA barcoding in plants: taxonomy in a new perspective. Curr Sci 99(11): 1530–1541.
Wilde WJJOD. 1967. A new combination and a new species in Saraca L. (Caesalpiniaceae). Blumea. 15(2): 392-395.
Wolfe KH, Modern CW, Palmer JD. 1992. Function and evolution of a minimal plastid genome from a non-photosynthetic parasitic plant. Proceed Nat Acad Sci 89:10648-10652.
Zuckerkandl E, Pauling L. 1965. Molecules as documents of evolutionary history. J Theoret Biol 8: 357–366.
Zuijderhoudt GFP. 1967. A revision of the genus Saraca L. (Legum. –CAES). Blumea 15(2): 413-425.