Abstract
A potentially diagnostic 18S rDNA (ribosomal DNA) gene was amplified reliably from red-listed ethnomedicinal species of Myristica and its wild and related genera. Individuals from nine species of Myristicaceae were utilized for the study. The sequences ranged from 1,767 to 1,794 nucleotide (nt) in length. The GC content (%) varied from 52.77 to 51.04. The frequencies (%) of nt were A (23.31), T (23.82), C (24.48) and G (28.39). The alignment of all sequences produced 195/1,516 variable sites and 1,257/1,516 conserved sites. Total numbers of single nucleotide polymorphism (SNP) sites found in the alignment were 146/1,516. Knema andamanica (Warb.) W.J. de Wilde was the most distinct that included 18 variable regions and 15 InDel with 27 SNP sites, specific to this species. The identified regions from nine species of Myristica and its wild and closely related genera were deposited in the GenBank Database (Accession numbers JN228257-JN228265). Comparison of morphological identifications and phylogenetic analysis indicated that the specimens were correctly assigned on the basis of a short stretch of 18S rDNA (~1,600 bp) making this a potentially useful marker for the rapid molecular assignment of an unknown related species also. Significant sequence homology ranging from 72 to 99 % was observed on comparison with 18S rDNA genes of other plants in the public domain. A comparison of intraspecific data information of nine 18S with that of 73 matK and 86 rbcL sequences from GenBank revealed that polymorphism, divergence and conservation is higher in 18S locus for Myristicaceae. Hence these markers may be utilized for phylogenetic analysis, evaluation of species richness during ecological surveys or for environmental assessments. These molecular markers are especially important due to the fact that the species studied are mostly vulnerable and red-listed with limited availability in endangered ecological niches.
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References
Arunachalam KD, Subhashini S (2011) Preliminary phytochemical investigation wound healing activity of Myristica andamanica leaves in Swiss Albino mice albino mice. J Med Plants Res 5:1095–1106
Atschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Cao H, Sasaki Y, Fushimi H, Komatsu K (2010) Authentication of Curcuma species (Zingiberaceae) based on nuclear 18S rDNA and plastid trnK sequences. Yao Xue Xue Bao 45:926–933
Chandran MDS, Mesta DK (2001) On the conservation of the Myristica swamps of the Western Ghats. In: Uma Shaanker R, Ganeshaiah KN, Kamaljit SB (eds) Forest genetic resources: status, threats and conservation strategies. Oxford and IBH Publishing Co Pvt. Ltd, New Delhi, pp 1–19
Conley J (2002) Nutmeg only a spice? In: Whitelaw WA (ed) Proceedings of the 11th annual history of medicine days, Health Science Centre, Calgary, pp 21–26
Dong W, Liu J, Yu J, Wang L, Zhou S (2012) Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7:e35071
Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle
Gray A (1996) Genetic diversity and its conservation in natural populations of plants. Biodiversity Lett 3:71–80
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Hebert PD, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270:313–321
Iyer IR, Jayaraman G, Ramesh A (2009) Direct somatic embryogenesis in Myristica malabarica Lam., an endemic, threatened medicinal species of Southern India and detection of phytochemicals of potential medicinal value. Indian J Sci Technol 2:11–17
Janovec JP, Harrison JS (2002) A morphological analysis of the Compsoneura sprucei complex (Myristicaceae), with a new combination for the Central American species Compsoneura mexicana. Syst Bot 27:662–673
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132
Krishnamoorthy B, Rema J (2001) Nutmeg and mace. In: Peter KV (ed) Hand book of herbs and spices. Wood head Publishing, Cambridge, pp 238–248
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452
Lynch M, Crease TJ (1990) The analysis of population survey data on DNA sequence variation. Mol Biol Evol 7:377–394
Manjunatha BK, Mankani KL, Mukunda SKR, Divakara BK, Divakara BK, Sridar PK (2011) Antioxidant and hepato protective effect of Myristica malabarica seed aril extracts on carbon tetrachloride induced hepatic damage. Global J Biotechnol Biochem 6:25–30
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Nei M, Miller JC (1990) A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data. Genetics 125:873–879
Newmaster SG, Fazekas AJR, Steeves AD, Janovec J (2008) Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Resour 8:480–490
Nickrent DL, Soltis DE (1995) A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Ann Mo Bot Gard 82:208–234
Patro BS, Bauri AK, Mishra S, Chatterjee S (2005) Antioxidant activity of Myristica malabarica extracts and their constituents. J Agric Food Chem 53:6912–6918
Porwal MC, Padalia H, Roy PS (2012) Impact of tsunami on the forest and biodiversity richness in Nicobar Islands (Andaman and Nicobar Islands), India. Biodivers Conserv 21:1267–1287
Rambaut A, Drummond AJ (2009) Tracer version 1.5. Available: http://tree.bio.ed.ac.uk/software/tracer/ Accessed 2012
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574
Sasaki Y, Fushimi H, Cao H, Cai SQ, Komatsu K (2002) Sequence analysis of Chinese and Japanese Curcuma drugs on the 18S rRNA gene and trnK gene and the application of amplification-refractory mutation system analysis for their authentication. Biol Pharm Bull 25:1593–1599
Sauquet H, Doyle JA, Scharaschkin T et al (2003) Phylogenetic analysis of Magnoliales and Myristicaceae based on multiple data sets: implications for character evolution. Bot J Linn Soc 142:125–186
Sharief MU (2007) Plants folk medicine of Negrito tribes of Bay Islands. Indian J Tradit Knowl 6:468–476
Sheeja TE, Rajesh Y, Krishnamoorthy B, Parthasarathy VA (2008) Optimization of DNA isolation and PCR parameters in Myristica sp. and related genera for RAPD and ISSR analysis. J Spices Aromat Crops 17:91–97
Sheeja TE, Sabeesh C, Shabna OV, Shalini RS, Krishnamoorthy B (2013 a) A comparative analysis of genetic diversity of wild and related genera of Myristica using RAPD and ISSR markers. J Spices Aromat Crops 22 (in press)
Sheeja TE, Anju PR, Shalini RS, Siju S, Dhanya K, Krishnamoorthy B (2013b) RAPD, SCAR and conserved 18S rDNA markers for a red-listed and endemic medicinal plant species, Knema andamanica (Myristicaceae). Physiol Mol Biol Plant. doi: 10.1007/s12298-013-0166-6
Soltis DE, Soltis PS, Nickrent DL et al (1997) Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann Mo Bot Gard 84:1–49
Soltis PS, Soltis DE, Wolf PG, Nickrent DL, Chaw SM, Chapman RL (1999) The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal? Mol Biol Evol 16:1774–1784
Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437–460
Tambat B, Vishwanath K, Chaithra GN, Hareesh TS (2006) Improved germination of Gymnacranthera canarica Warb, an endangered, endemic tree species of Myristica swamps, Western Ghats. Seed Sci Technol 34:625–630
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276
Wiart CR (2006) Ethnopharmacology of medicinal plants: Asia and the Pacific. In: Jennifer Hackworth (ed) Humana Press Inc, New Jersey
Zachariah TJ, Leela NK, Maya KM, Rema J, Mathew PA, Vipin TM, Krishnamoorthy B (2008) Chemical composition of leaf oils of Myristica beddomeii (King), Myristica fragrans (Houtt.) and Myristica malabarica (Lamk.). J Spices Aromat Crops 17:10–15
Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas, Austin http://zipcodezoo.com/Key/Plantae/Myristica_Genus.asp
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Sheeja, T.E., Rosana, O.B., Swetha, V.P. et al. The 18S rDNA gene discriminates between red-listed and unexplored ethnomedicinal species of Myristicaceae restricted to humid tropics of India. Genet Resour Crop Evol 61, 523–535 (2014). https://doi.org/10.1007/s10722-013-0060-7
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DOI: https://doi.org/10.1007/s10722-013-0060-7