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Molecular phylogeny in Indian Tinospora species by DNA based molecular markers

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Abstract

The phylogenetic relationships among the three species of Tinospora found in India are poorly understood. Morphology does not fully help to resolve the phylogeny and therefore a fast approach using molecular analysis was explored. Two molecular approaches viz Random Amplified Polymorphic DNA (RAPD) assay and restriction digestion of ITS1-5.8S-ITS2 rDNA (PCR-RFLP) were used to evaluate the genetic similarities between 40 different accessions belonging to three species. Of the 38 random primers used only six generated the polymorphism, while as three out of 11 restriction enzymes used gave polymorphic restriction patterns. The average proportion of polymorphic markers across primers was 95%, however restriction endonucleases showed 92% polymorphism. RAPD alone was found suitable for the species diversions. In contrast PCR- RFLP showed bias in detecting exact species variation. The correlation between the two markers was performed by Jaccard's coefficient of similarity. A significant (r= 0.574) but not very high correlation was obtained. Further to authenticate the results obtained by two markers, sequence analysis of ITS region of ribosomal DNA (ITS1 and ITS2, including 5.8S rDNA) was performed. Three independent clones of each species T. cordifolia, T. malabarica and T. crispa were sequenced. Phylogenetic relationship inferred from ITS sequences is in agreement with RAPD data.

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References

  • B. G Baldwin (1992) ArticleTitlePhylogenetic utility of the internal transcribed sequences of nuclear ribosomal DNA in plants: an example from the Compositae Molec. Phylogenet. Evol 1 3–16 Occurrence Handle1342921 Occurrence Handle1:CAS:528:DyaK3sXms1eksLo%3D

    PubMed  CAS  Google Scholar 

  • B. G Baldwin (1993) ArticleTitleMolecular phylogenetics of Calycadenia (Compositae) based on ITS sequences of nuclear ribosomal DNA: chromosomal and morphological evolution reexamined Amer. J. Bot 80 222–238 Occurrence Handle1:CAS:528:DyaK3sXksVGgt7o%3D

    CAS  Google Scholar 

  • B. G Baldwin M. J Sanderson J. M Porter M. F Wojciechowski C. S Campbell M. J Donoghue (1995) ArticleTitleThe ITS region of nuclear ribosomal DNA a valuable source of evidence on angiosperms Mol. Bot. Genet 82 247–277

    Google Scholar 

  • R. J Bayer D. E Soltis S. P Soltis (1996) ArticleTitlePhylogenetic inferences in Antennaria (Asteraceae: Gnaphalieae: Cassininae) base on seqence from nuclear ribosomal DNA internal transcribed spacer (ITS)1 Amer. J. Bot 83 IssueID4 516–527 Occurrence Handle1:CAS:528:DyaK28XjtVWltLY%3D

    CAS  Google Scholar 

  • G Bernardi B Olofsson J Filipski M Zerial J Salinas G Cuny M Meunier-Rotival F Rotival (1985) ArticleTitleThe mosaic genome of warm blooded vertebrates Science 228 953–958 Occurrence Handle4001930 Occurrence Handle1:CAS:528:DyaL2MXksVyquro%3D

    PubMed  CAS  Google Scholar 

  • D Botstein R. L White M Skolnick R. W Davis (1980) ArticleTitleConstruction of genetic linkage map in man using restriction length polymorphism Am. J. Hum. Genet 32 314–331 Occurrence Handle6247908 Occurrence Handle1:CAS:528:DyaL3cXkvFamtbc%3D

    PubMed  CAS  Google Scholar 

  • Chadha Y.R. (1976) Tinospora In: The wealth of India. Publication and information Directorate, C.S.I.R New Delhi India, 10, pp. 251.

  • S. L Dellaporta J Wood J. B Hicks (1983) ArticleTitleA plant DNA minipreparation: Version II Plant Mol. Biol. Reptr 1 19–21 Occurrence Handle1:CAS:528:DyaL2cXksFWhtrk%3D Occurrence Handle10.1007/BF02712670

    Article  CAS  Google Scholar 

  • J. B Dos Santos J Nienhuis P Skroch J Tivang M. K Slocum (1994) ArticleTitleComparison of RAPD and RFLP genetic markers in determinating genetic similarity among Brassica oleracea L. genotypes Theor. Appl. Genet 87 909–915 Occurrence Handle1:CAS:528:DyaK2cXlslGgtL4%3D

    CAS  Google Scholar 

  • G. A Dover (1986) ArticleTitleMolecular drive in multigene families: how biological novelties arise, spread and are assimilated Trends Genet 6 159–165

    Google Scholar 

  • J. J Doyle R. N Beachy (1985) ArticleTitleRibosomal gene variation in soybean (Glycine) and its relatives Theor. Appl. Genet 70 369–376 Occurrence Handle1:CAS:528:DyaL2MXlsFOmsL8%3D

    CAS  Google Scholar 

  • R. K Hamby E. A Zimmer (1992) Ribosomal RNA as phylogenetic tool in plant systematics P. S Soltis D. E Natis J.J Doyle (Eds) Molecular systematics of plants Chapman and Hall London 50–91

    Google Scholar 

  • M. A Hershkovitz L. A Lewis (1996) ArticleTitleDeep level diagnostic value of the rDNA-ITS region Molec. Biol. Evol 13 IssueID9 1276–1295 Occurrence Handle8896380 Occurrence Handle1:CAS:528:DyaK28Xms1Siu7Y%3D

    PubMed  CAS  Google Scholar 

  • J Jobst K King V Hemleben (1998) ArticleTitleMolecular evolution of internal transcribed spacers (ITS1 and ITS2) and phylogenetic relationships among species of the family Cucurbitaceae Molec. Phylogenet. Evol 9 204–219 Occurrence Handle9562980 Occurrence Handle1:CAS:528:DyaK1cXivVaitbk%3D

    PubMed  CAS  Google Scholar 

  • P Karvonen O Savolainen (1993) ArticleTitleVariation and inheritance of ribosomal DNA in Pinus sylvestris L (Scots Pine) Heredity 71 614–622 Occurrence Handle1:CAS:528:DyaK2cXitFaksbw%3D

    CAS  Google Scholar 

  • S. A Khan D Hussain E Askari J Stewart K.A Malik Y Zafar (2000) ArticleTitleMolecular phylogeny of Gossypium species by DNA fingerprinting Theor. Appl. Genet 101 931–938 Occurrence Handle10.1007/s001220051564 Occurrence Handle1:CAS:528:DC%2BD3cXosFygsrs%3D

    Article  CAS  Google Scholar 

  • R. C Lewontin (1972) ArticleTitleThe apportionment of human diversity Evol. Biol 6 381–398

    Google Scholar 

  • R Maurya (1996) Chemistry of Tinospora cordifolia species S.S Handa M.K Kual (Eds) Supplements to cultivation and utilization of medicinal plants Regional Research Laboratory Jammu 413–422

    Google Scholar 

  • D Menancio-Hautea C. A Fatokun L Kumar D Denesh N. D Young (1993) ArticleTitleComparative genome analysis of mungbean (Vigna radiata (L.) Wilczek) and cowpea (Vigna unguiculata (L.) Walpers) using RFLP mapping data Theor. Appl. Genet 86 797–810 Occurrence Handle10.1007/BF00212605 Occurrence Handle1:CAS:528:DyaK2cXivFWjtrk%3D

    Article  CAS  Google Scholar 

  • M Nei (1987) Molecular evolutionary genetics Columbia University Press New York 276–290

    Google Scholar 

  • T Ouellet K. A Seifert (1993) ArticleTitleGenetic characterization of Fusarium graminearum strains using RAPD and PCR amplification Phytopathology 83 1003–1007 Occurrence Handle1:CAS:528:DyaK2cXhtVWksbk%3D

    CAS  Google Scholar 

  • M Pelandakis S Serre P Pernin (2000) ArticleTitleAnalysis of the 5.8S rRNA gene and internal transcribed spacers in Naegleria spp. and in N. fowleri J. Eukaryot. Micrbiol 47 116–121 Occurrence Handle1:CAS:528:DC%2BD3cXisFertbg%3D

    CAS  Google Scholar 

  • A Quijada A Liston P Delgado A Vazquez-Lobo E. R Alvarez-Buylla (1997) ArticleTitleVariation in nuclear ribosomal DNA internal transcribed spacer (ITS) region of Pinus rzedowskii revealed by PCR-RFLP Theor. Appl. Genet 96 539–544

    Google Scholar 

  • C. E Ritland K Ritland N. A Strauss (1993) ArticleTitleVariation in the ribosomal internal transcribed spacers (ITS1 and ITS2) among eight taxa of the Mimulus guttatus species complex Molec. Biol. Evol 10 1273–1288 Occurrence Handle7904042 Occurrence Handle1:CAS:528:DyaK2cXntlKisw%3D%3D

    PubMed  CAS  Google Scholar 

  • C. E Ritland N. A Strauss (1993) ArticleTitleHigh evolutionary divergence of the 5.8S rDNA internal transcribed spacer in Mimulus glaucescens (Scrophulariaceae) relative to other higher plant species Plant. Molec. Biol 9 691–520

    Google Scholar 

  • F. J Rohlf (1993) NTSYS-pc. Numerical taxonomy and multivariate analysis system: version 1.8 Applied Biostatistics New York

    Google Scholar 

  • N Saitou M Nei (1987) ArticleTitleThe neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol 4 406–425 Occurrence Handle3447015 Occurrence Handle1:STN:280:BieC1cbgtVY%3D

    PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch E. F, Maniatis T (1989) Molecular cloning: a lab manual, Cold Spring Harbour Laboratory. New York USA.

  • B. A Schaal SuffixJr G. H Learn (1988) ArticleTitleRibosomal DNA variation within and among palnt populations Ann. Missouri. Bot. Gard 75 1207–1216

    Google Scholar 

  • G. J Scoles B. S Gills Z. Y Xin B. C Clarke C. L Mc Intyre C Chapman R Apples (1987) ArticleTitleFrequent duplication and deletion events in 5S rRNA genes and the associated spacer regions of Triticeae Plant Syst. Evol 160 105–122

    Google Scholar 

  • S. K Sharma I. K Dawson R Waugh (1995) ArticleTitleRelationship among cultivated and wild lentils revealed by RAPD analysis Theor. Appl. Genet 85 697–701

    Google Scholar 

  • T. R Sharma S Jana (2002) ArticleTitleSpecies relationships in Fagopyrum by PCR-based DNA fingerprinting Theor. Appl. Genet 105 306–312 Occurrence Handle12582533 Occurrence Handle1:CAS:528:DC%2BD38Xntlejsr8%3D

    PubMed  CAS  Google Scholar 

  • P. S Soltis R. K Kuzoff (1993) ArticleTitleITS sequences variation within and among population of Lomatium greyi and L laevigatum (Umbelliferae) Mol. Phylogenet. Evol 2 166–170 Occurrence Handle8025723 Occurrence Handle1:CAS:528:DyaK2cXitFaktrY%3D

    PubMed  CAS  Google Scholar 

  • J Souframanien A Josi G Krishna (2003) ArticleTitleIntraspecific variation in the internal transcribed spacer of rDNA in black gram (Vigna mungo (L.) Hepper) Curr. Sci 85 791–802

    Google Scholar 

  • W Stephan (1989) ArticleTitleTandem repetitive non coding DNA: forms and forces Molec. Biol. Evol 6 198–212 Occurrence Handle2716519 Occurrence Handle1:CAS:528:DyaL1MXktlGht74%3D

    PubMed  CAS  Google Scholar 

  • Y Suh L. B Thien H. E Reeve E. A Zimmer (1993) ArticleTitleMolecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae Amer. J. Bot 80 1042–1055 Occurrence Handle1:CAS:528:DyaK2cXivFCgsbk%3D

    CAS  Google Scholar 

  • S. D Tanksley N.D Young A. H Paterson M. W Bonierbale (1989) ArticleTitleRFLP mapping in plant breeding-new tool for an old science Bio/Technology 7 257–264 Occurrence Handle10.1038/nbt0389-257 Occurrence Handle1:CAS:528:DyaL1MXltV2kt7k%3D

    Article  CAS  Google Scholar 

  • Verma V., Ahmad S. M., Ganaie M. M., Basir S. F., Reshi Z., Qazi G. N. (2004) Ribosomal genes in plants – Phylogenetic importance. In: Advances in Biotechnology (In press).

  • J Welsh M McClelland (1990) ArticleTitleFingerprinting of Theobroma clones using randomly amplified polymorphic primers Nucleic Acids Res 18 6531–721

    Google Scholar 

  • W.J Wilbur D.J Lipman (1983) ArticleTitleRapid similarity searches of nucleic acid and protein data banks Proc. Natl. Acad. Sci. USA 80 727–730

    Google Scholar 

  • T. J White T Bruns S Lee J Taylor (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics M Innis D Gelfand J Sninsky T White (Eds) PCR protocols: a guide to methods and applications Academic Press San Diego 315–322

    Google Scholar 

  • J. G. K Williams A. R Kubelik K. J Livak J. A Rafalski S. V Tingey (1990) ArticleTitleDNA polymorphisms amplified by arbitrary primers are useful as genetic markers Nucleic Acids Res 18 6531–6535 Occurrence Handle1979162 Occurrence Handle1:CAS:528:DyaK3MXjslWmsA%3D%3D

    PubMed  CAS  Google Scholar 

  • Y Yokota T Kawata Y Iida A Kato S Tanifuji (1989) ArticleTitleNucleotide sequences of the 5.8S rRNA gene and internal transcribed spacer regions in carrot and broad bean ribosomal DNA J. Molec. Evol 29 294–301 Occurrence Handle2514271 Occurrence Handle1:CAS:528:DyaK3cXktVWgsrY%3D

    PubMed  CAS  Google Scholar 

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  1. Biotechnology Division, Regional Research Laboratory, Canal Road, Jammu Tawi, 180001, India

    S. M. Ahmed, V. Verma, P. H. Qazi, M. M. Ganaie, S. K. Bakshi & G. N. Qazi

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  1. S. M. Ahmed
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  2. V. Verma
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  3. P. H. Qazi
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Correspondence to V. Verma.

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Ahmed, S., Verma, V., Qazi, P. et al. Molecular phylogeny in Indian Tinospora species by DNA based molecular markers. Plant Syst. Evol. 256, 75–87 (2005). https://doi.org/10.1007/s00606-004-0293-1

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