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Withania somnifera: Diversity and phylogeny - An overview

Masood Majaz Ganaie, Pervaiz Hassan Qazi, Vijeshwer Verma, Zafar Ahmad Reshi, Ab. Qayoom Mir, Vaseem Raja

Abstract


The diversity and phylogenetic relationships within Solanaceae are interesting. Withania, despite being an important genus of the family, has not found proper attention for such studies and even species delimitation within the genus is debatable. Different authors at different points of times classified Withania somnifera into different morphological forms and split it into two different species. Similarly, there are various uncertainties about phylogenetic relationships below the family level in Solanaceae and Withania. In the present study, morphological and molecular data have been used to overview the diversity and phylogeny of Withania, particularly W. somnifera. The morphological studies, RAPD, ISSR, cytochrome P450 sequence, derived primers, SSR analogues, and ITS sequence data support that the species has a lot of polymorphism bifurcated into two well-demarcated varieties. However, there is no conclusive support for dividing the species into more than two forms or splitting the species into two different species, rbcL gene sequence data supports a close relationship of the genus with Physalis and associated genera.

Keywords


Withania; Solanaceae; polymorphism; phylogeny; PCR; sequence

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Ahmad, Syed M., Masood M. Ganaie, Pervaiz H. Qazi, Vijeshver Verma, Seemi F. Basir, and Ghulam N. Qazi. "Rapid DNA isolation protocol for angiospermic plants." Bulgar J Plant physiol 30 (2004): 25-33.

Ahmed, S. M., V. Verma, P. H. Qazi, M. M. Ganaie, S. K. Bakshi, and G. N. Qazi. "Molecular phylogeny in Indian Tinospora species by DNA based molecular markers." Plant Systematics and Evolution 256, no. 1-4 (2005): 75-87.

Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic acids research 25, no. 17 (1997): 3389-3402.

Atal, C K. and Schwarting. A.E. “Interspecific varaiability in Withania somnifera” I. Preliminary survey. Llyoida. 25 (1962.) 78-88.

Axelius, B. “The phylogenetic relationships of the physaloid genera (Solanaceae) based on morphological data. American Journal of Botany. 83 (1996.) 118-124.

Baldwin, B. G., M. J. Sanderson, J. M. Porter, M. F. Wojciechowski, C. S. Campbell and M. J. Donoghue. “The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden. 82 (1995) 247-277.

Bahulikar, R. A., D. Stanculescu, C. A. Preston and I. T. Baldwin. ”ISSR and AFLP analysis of the temporal and spatial population structure of the post-fire annual, Nicotiana attenuata, in SW Utah. BMC Ecology. 4 (2004) 12-21.

Bayer, J. R., E. D. Solitis and S. P. Solitis. “Phylogenetic inferences in Antennaria (Asteraceae: Gnaphalieae: Cassininae) based on sequences from nuclear ribosomal DNA internal transcribed Spacers (ITS1)”. American Journal of Botany. 83 (1996.) 516-527.

Bell, C.D. “Preliminary phylogeny of Valerianaceae (Dipsacales) inferred from nuclear and chloroplast DNA sequence data”. Molecular Phylogenetics and Evolution. 31 (2004) 340-350.

Bornet, B. and M. Branchard. “Non-anchored inter simple sequence repeat (ISSR) markers: Reproducible and specific tools for genome fingerprinting”. Plant Molecular Biology Reporter.19 (2001) 209-215.

Bornet, B., C. Muller, F. Paulus and M. Branchard. “Highly informative nature of inter simple sequence repeat (ISSR) sequences amplified using tri- and tetra-nucleotide primers from DNA of cauliflower (Brassica oleracea var. botrytis L”. Genome. 45 (2002) 890-896.

Brouat, C., D. McKey and E. J. P. Douzery. “Differentiation in a geographical mosaic of plants coevolving with ants: Phylogeny of the Leonardoxa africana complex (Fabaceae: Caesalpinioideae) using amplified fragment length polymorphism markers”. Molecular Ecology. 13 (2004) 1157-1171.

Campbell, D., P. Duchense and L. Bernautchez. “AFLP utility for population assignment studies: Analytical assignment and empirical comparison with microsatellites”. Molecular Ecology. 12 (2003) 1979-1991.

Cardoso, S. R. S., N. B. Eloy, J. Provan, M. A. Cardoso and P. D. G. Ferreira. “Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis”. Molecular Ecology. 9 (2000) 1753-1760.

Cervera, M. T., J. A. Cabezas, B. Simon, Z. J. M. Martinez, F. Beitia and J. L. Cenis. “Genetic relationships among biotypes of Bemisia tabaci (Hemiptera: Aleyrodidae) based on AFLP analysis”. Bulletin of Entomological Research. 90 (2000)391-396.

Chase, M. W. S. Knapp, A. V. Cox, J. J. Clarkson, Y. Butsko, J. Joseph, V. Savolainen and A. S. Parokonny. “Molecular systematics, GISH, the origin of hybrid taxa in Nicotiana (Solanaceae). Ann. Bot. 92 (2003.) 107-127.

Chiang, T. Y., Y. C. Chiang and C. H. Chou. “Complete nucleotide sequence of the intergenic spacer between 25S and 17S rDNA in Miscanthus sinensis var. glaber”. Botanical Bulletin of Academia Sinica. 39 (1998.) 241-244.

Chong, L. K, S. G. Tan, K. Yusoff and S. S. Siraj. “Identification and characterization of Malaysian river catfish, Mystus nemurus (C&V): RAPD and AFLP analysis.” Biochemical Genetics. 38 (2000.) 63-76.

Chou, C. H. and C. C. Tsai. “Genetic variation in the intergenic spacer of ribosomal DNA of Imperata cylindrica (L.) Beauv. var. major (Cogongrass) populations in Taiwan”. Botanical Bulletin of Academia Sinica. 40 (1999) 319-327

Clark, C. B. “Solanaceae. In: The Flora of British India. Vol. IV. Ed. J. D. Hooker. L. Reeve & Co. Ltd”. The Oast House, Book, Ashford, Kent. 1883.

Clegg, M. T. “Chloroplast gene sequences and the study of plant evolution”. Proceedings of National Academy of Sciences, USA. 90 (1993) 363-367.

Clegg, M. T. and S. E. Curtis, Molecular evolution of chloroplast DNA sequences. Molecular Biology and Evolution. 1 (1984.) 291-301.

Coulibaly, S., R. S. Pasquet, R. Papa and P. Gepts. “AFLP analysis of the phenetic organization and genetic diversity of Vigna unguiculata L. Walp. reveals extensive gene flow between wild and domesticated types”. Theoretical and Applied Genetics. 104 (2002) 358-366.

Dalbo, M. A., G. N. Ye, N. F. Weeden, W. F. Wilcox and B. I. Reisch. “Marker-assisted selection for powdery mildew resistance in grapes”. Journal of the American Society for Horticultural Science. 126 (2001) 83-89.

D’Arcy, W. D., R. C. Keating, Z.-Y. Zhang and C.-I. Peng. “The genus Tubocapsicum (Solanaceae)”. Botanical Bulletin of Academia Sinica. 42 (2001) 67-84.

Després, L., L. Gielly, B. Redoutet and P. Taberlet. “Using AFLP to resolve phylogenic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability”. Molecular Phylogenetics and Evolution. 27 (2003.) 185–196.

Fay, M. F., R. G. Olmstead, J. E. Richardson, E. Santiago, G. T. Prance and M. W. Chase. “Molecular data support the inclusion of Duckeodendron cestroides in Solanaceae”. Kew Bulletin. 53 (1998) 203-212.

Heiser, C. B. Jr. Nightshades: “The Paradoxical Plants”. W. H. Freeman, San Francisco, CA. 1969.

Hershkovitz, M. A. and L. A. Lewis. “Deep-level diagnostic value of the RDNA-ITS region”. Mol. Biol. Evol. 13 (1996) 1276-1295.

Hershkovitz, M. A. and Zimmer, E. A. “Conservation patterns in angiosperm rDNA ITS2 sequences”. Nucleic Acids Research. 24 (1996) 2857-2867.

Hodkinson, T. R., M. W. Chase and S. A. Renvoize. “Characterization of a genetic resource collection for Miscanthus (Saccharinae, Andropogoneae, Poaceae) using AFLP and ISSR PCR”. Annals of Botany. 89 (2002) 627-636.

Hodkinson, T. R., S. A. Renvoize, G. N. Chonghaile, C. Stapleton and M. W. Chase. “A comparison of ITS nuclear rDNA sequence data and AFLP markers for phylogenetic studies in Phyllostachys (Bambusoideae, Poaceae)”. Journal of Plant Research. 113 (2000) 259–269.

Hoot, S. B. and A. W. Douglas “Phylogeny of the Proteaceae based on atpB and atpB-rbcL intergenic spacer region sequences”. Australian Systematic Botany. 11 (1998) 301-320.

Jobes, D. V. and L. B. Thien. “A conserved motif in the 5.8S ribosomal RNA (rRNA) gene is a useful diagnostic marker for plant internal transcribed spacer (ITS) sequences”. Plant Molecular Biology Reporter. 15 (1997). 326-334.

Kaul, K. N. “The origin, distribution, cultivation of ashwagandha the so called Withania somnifera of Indian literature. [In: Symposium on the Utilization of Indian Medicinal Plants, LucknoW. Council of Scientific and Industrial Research, New Delhi]: (1957) 7-8.

Kaul, M. K., A. Kumar and A. Sharma. “Reproductive biology of Withania somnifera (L.)” Dunal. Current Science. 88 (2005) 1375-1377.

Kim, M. S., P. H. Moore, F. Zee, M. M. M. Fitch, D. L. Steiger, R. M. Manshardt, R. E. Paull, R. A. Drew, T. Sekioka and R. Ming. “Genetic diversity of Carica papaya as revealed by AFLP markers”. Genome. 45 (2002) 503–512.

Knapp, S. “Tobacco to tomatoes: A phylogenetic perspective on fruit diversity in the Solanaceae”. Journal of Experimental Botany. 53 (2002) 2001-2022.

Knapp, S., L. Bohs, M. Nee and M. Spooner. “Solanaceae- a model for linking genomics with biodiversity”. Comparative and Functional Genomics. 5 (2004). 285-291.

Larkin, J. C. “Isolation of a cytochrome P450 homologue preferentially expressed in developing inflorescences of Zea mays”. Plant Molecular Biology. 25 (1994) 343–353.

Lavie, D., I. Kirson and A. Abraham. “Chemical approach to genetics”. Israel Journal of Chemistry. 14 (1975). 60-68.

Lewinton, R. C. “The apportionment of human diversity”. Evolutionary Biology. 6 (1972) 381-398.

Li, A. and S. Ge. “Genetic variation and clonal diversity of Psammochloa villosa (Poaceae) detected by ISSR markers”. Annals of Botany. 87 (2001). 585-590.

Liu, J. S. and C. L. Schardl, 1994. A conserved sequence in internal transcribed spacer-1 of plant nuclear ribosomal-RNA genes. Plant Molecular Biology. 26: 775-778.

Mackill, D. J., Z. Zhang, E. D. Redona and P. M. Colowit. “Level of polymorphism and genetic mapping of AFLP markers in rice. Genome. 39 (1996). 969–977.

Milbourne, D., R. Meyer, J. E. Bradshaw, E. Baird, N. Bonar, J. Provan, W. Powell and R. Waugh. “Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato”. Molecular Breeding. 3 (1997) 127-136.

Malik, S., B. A. Mir, H. K. Singh, M. Choudhary, S. N. Raina and S. B. Babbar. “DNA Barcodes Distinguish Withania somnifera and Withania ashwagandha”. Proceedings of the National Academy of Science, India Section B Biological Science: 88 (2018) 1413-1424.

Miyao, A., H. Zhong, L. Monna, M. Yano, K. Yamamoto, I. Havukkala, Y. Minobe and T. Saaki.” Characterization, genetic mapping of simple sequence repeats in the rice genome”. DNA Research. 3 (1996). 233-238.

Money, T., S. Reader, L. J. Qu, R. P. Dunford and G. Moore. “AFLP-based mRNA fingerprinting. Nucleic Acids Research. 24 (1996). 2616-2617.

Naylor, G. J. P. and W. M. Brown. C.”Structural biology and phylogenetic estimation. Nature. 388 (1996) 527-528.

Naylor, G. J. P. and W. M. Brown. 1998. “Amphioxus mitochondrial DNA, chordate phylogeny and the limits of inference based on comparisons of sequences”. Systematic Biology. 47 (1998). 61-76.

Negi, M. S., A. Singh and M. Laxmikumaran. “Genetic variation and relationship among and within Withania species as revealed by AFLP markers”. Genome. 43 (2000) 975-980.

Negrisolo, E., S. Maistro, M. Incarbone, I. Moro, L. D. Valle, P. A. Broady and C. Andreoli’ Morphological convergence characterizes the evolution of Xanthoph-yceae (Heterokontophyta): Evidence from nuclear SSU rDNA and plastidial rbcL genes”. Molecdcular Phylogenetics and Evolution. 33 (2004). 156-170.

Ohkawa, H., H. Imaishi, N. Shiota, T. Yamada, H. Inui and Y. Ohkawa. “Molecular mechanisms of herbicide resistance with special emphasis on cytochrome P450 mono-oxigenases”. Plant Biotechnology. 15 (1998.) 173–178.

Oleszczuk, S., J. Zimny and P. T. Bednarek. “The application of the AFLP method to determine the purity of homozygous lines of barley (Hordeum vulgare L.)”. Cellular and Molecular Biology Letters. 7(2002) 777–783.

Olmstead, R. G., J. A. Sweere, R. E. Spangler, L. Bohs and J. D. Palmer. “Phylogeny and provisional classification of the Solanaceae based on chloroplast DNA. [In: M. Nee, D. E. Symon, R. N. Lester and Jessop (eds.). Solanaceae IV: Advances in Biology and Utilization. Royal Botanical Garden, Kew, UK]: (1999) 111–137.

Olmstead, R. G. and J. D. Palmer. “A chloroplast DNA phylogeny of the Solanaceae: Subfamilial relationships and character evolution”. Annals of the Missouri Botanical Garden. 79 (1992). 346-360.

Olmstead, R. G. and J. A. Sweere. “Combining data in phylogenetic systematics: An empirical approach using three molecular data sets in the Solanaceae”. Systematic Biology. 43 (1994) 467-481.

Powell, W., M. Morgante, C. Andre, M. Hanafey, J. Vogl, S. Tingey, and A. Rafalaski. ”The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis”. Molecular Breeding. 3 (1996) 225-238.

Qui, Y.L., J.Lee, F. Bernasconi-Quadroni, D.E. Soltis, P. S. Soltis, M. Zaner, E. A. Zimmer, Z. Chen, V. Savolainen and M. W. Chase. “The earliest angiosperms”. Nature. 402 (1999). 404-407.

Reddy. M. P. N. Sarla and E. A. Siddiq. “Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding”. Euphytica. 128 (2002) 9-17.

Reichmann, J.L., J. Heard, G. Martin, L. Reuber, C. Z. Jiang, J. Keddie, L. Adam. O. Pineda, O. J. Ratcliffe, R. R. Samaha, R. Creelman, M. Pilgrim, P. Broun, J. Z. Zhang, D. Ghandehari, B. K. Sherman, G.-L. Yu. “Arabidiopsis transcription factors: b Genome wide comparative analysis among eukaryotes”. Science. 290 (2001) 2105-2110.

Ridout, C. J. and P. Donini. “Use of AFLP in cereals research. Trends in Plant Science. 4 (1999) 76-79.

Saitou, N. and M. Nei. “The neighbour-joining method: Anew method for reconstructing phylogenetic trees”. Mol. Biol. Evolution. 4 (1987) 406-425.

Savolainen, V., M. W. Chase, S. B. Hoot, C. M. Morton, D. E. Soltis, C. Bayer, M. Fay, A. Y. de Bruijn, S. Sullivan, and Y. L. Qiu. “Phylogenetics of flowering plants based on a combined analysis of plastid atpB and rbcL gene sequences”. Systematic Biology. 49 (2000) 306-362.

Scotland, R. W., R. G. Olmstead and J. R Bennett. “Phylogeny Reconstruction: The Role of Morphology”. Systematic Biology. 52(2003) 539-548.

Scott, V., S. V. Tingey and J. P. del Tufo. “Genetic analysis with random amplified polymorphic DNA markers”. Plant Physiology. 101(1993) 349-352.

Shalk, M., S. Nedelkiana, G. Schoh, Y. Batard and D. Werck-Reichhart. “Roles of unusual amino-acids residues in the proximal and distal heme- regions of a plant P450, CYP73A1”. Biochemistry. 38 (1999) 6093-6103.

Shalk, M., S. Nedelkina, G. Schoch, Y. Batard and D. Werck-Reichhart. “Role of unusual aminoacid residues in the proximal and distal heme regions of a plant P450, CYP73A1”. Biochemistry. 38(1999). 6093-6103.

Shan, X., T. K. Blake and L. E. Talbert. “Conversion of AFLP markers to sequence-specific PCR markers in barley and wheat”. Theoretical and Applied Genetics. 98 (1999). 1072-1078.

Shinozaki, K., M. Ohme, M. Tanaka, T. Wakasugi, N. Hayashida, T. Matsubayashi, N. Zaita, J. Chunwongse, J. Obokata, K. Yamaguchi-Shinozaki, C. Ohto, K. Torazawa, B. Y. Meng, M. Sugita, H. Deno, T. Kamogashira, K. Yamada, J. Kusuda, F. Takaiwa, A. Kata, N. Tohdoh, H. Shimada and M. Sugiura. “The complete nucleotide sequence of tobacco chloroplast genome: Its gene organization and expression”. EMBO Journal. 5 (1986).2043-2049.

Singh, S. and S. Kumar. “Withania somnifera. The Indian Ginseng Ashwagandha”. Central Institute of Medicinal and Aromatic Plants (CIMAP), LucknoW. 226015, India (1998).

Small, R. L., J. A. Ryurn, R. C. Cronn, T. Seelanan and J. F. Wendel. “The tortoise and the hare: Choosing between non-coding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group”. American Journal of Botany. 85 (1998). 1301-1315.

Smelcerovic, A., V. Verma, M. Spitller, S. M. Ahmad, S. C. Puri and G. N. Qazi. “Phytochemical analysis and genetic characterization of six Hypericum species from Serbia”. Phytochemistry. 67 (2006). 171-177.

Sobral, B. W. S. and R. J. Honeycutt. “High output genetic mapping of polyploids using PCR-generated markers”. Theoretical and Applied Genetics. 86 (1993) 105-112.

Soltis, D. E., P. S. Saltis, M. E. Mort, M. W. Chase, V. Savolainen, S. B. Hoot and C. M. Morton. “Inferring complex phylogenies using parsimony: An empirical approach using three large datasets for angiosperms”. Systematic Biology. 47 (1998.) 32-42.

Soltis, D. E. M. E. Mort, P. S. Soltis, C. Hibsch-Jetter, E. A. Zimmer and D. Morgan. “Phylogenetic relationships of the enigmatic angiosperm family Podostemaceae inferred from 18SrDNA and rbcL sequence data”. Molecular Phylogenetics and Evolution. 11 (1999). 261-272.

Soltis, D. E. and R. K. Kuzoff. “ITS sequences variation within and among population of Lomatium greyi and L. laevigatum (Umbelliferae)”. Molecular Phylogenetics and Evolution. 2(1993). 166-170.

Somerville, C. and S. Somerville. “Plant functional genomics. Science. 285 (1999.) 380-383.

Song, B. K., M. M. Clyde, R. Wickneswari and M. N. Normah. 2000. Genetic relatedness among Lansium domesticum accessions using RAPD markers. Annals of Botany. 86: 299-307.

Stebbins, G. L. 1974. Flowering plants: Evolution Above the Species Level. Belknap, Cambridge, MA.

Ubi, B. E., F. Masahiro; E. Masumi, M. Yoshiro and K. Toshinori. “AFLP variation in tetraploid cultivars of rhodes grass (Chloris gayana Kunth)”. Grassland Science. 46 (2000) 242-248.

Verma, V., S. M. Ahmad, M. M. Ganaie, S. F. Basir, Z. Rishi, and G. N. Qazi, Ribosomal genes in plants: Phylogenetic importance. [In: P. C. Trivedi (ed.). Advances in Biotechnology. Agrobios India, New Delhi.]: (2005). 241-254.

Welsh, J. and M. McClelland. “Fingerprinting genomes using PCR with arbitrary primers”. Nucleic Acids Research. 18 (1990). 7213. 7218.

White, T. J., T. Bruns, S. Lee and J. Taylor. “Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. [In: M. Innis, D. Gelfand, J. T. Sninsky and J. White (eds.). PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA]: (1990). 315–322.

Whitson, M. and P. S. Manos. “Untangling Physalis (Solanaceae) from the Physaloids: A two-gene phylogeny of Physalinae. Systematic Botany. 30 (2005) 216–230.

Wong, C., R. Kiew, J. P. Loh, L. H. Gan, O. Set, S. K. Lee, S. Lum and Y. Y. Gan. “Genetic diversity of the wild Musa acuminata Colla in Malaysia as evidenced by AFLP”. Annals of Botany. 88(2001). 1017-1025.

Yamanaka, S., E. Suzuki, M. Tanaka, J. A. Watanabe and K. N. Watanabe. “Assessment of cytochrome P450 sequences offers a useful tool for determining genetic diversity in higher plant species”. Theoretical and Applied Genetics. 108 (2003). 1-9.

Zerega, N. J. C., S. Mori, C. Lindqvist, Q. Zheng and T. J. Motley. “Using amplified fragment length polymorphisms (AFLP) to identify black cohosh (Actaea racemosa)”. Economic Botany. 56 (2000). 154–164.




DOI: https://doi.org/10.5281/aps.2021.10.1.2



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