Subfamilial relationships within solanaceae as inferred from atpaβ-rbcL intergenic spacer

Pakistan Journal of Botany

Volumn 46, Issue 2, 2014, Pages 585-590

  Jamil, Ishrat ^a   Qamarunnisa, Syeda ^a   Azhar, Abid ^a   Shinwari, Zabta K ^b   Ali, Syed Irtifaq ^a   Qaiser, Muhammad ^a  

^a UNIVERSITY OF KARACHI   (Pakistan)

^b QUAID I AZAM UNIVERSITY   (Pakistan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84896440754     PISSN: 05563321     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (49)

1. Abbas, Q., R. Qureshi, A.U.N. Naqvi, S.W. Khan and I. Hussain. 2013. Floristic inventory and ethnobotanical study of the Naltar valley (Karakoram range), Gilgit, Pakistan. Pak. J. Bot., 45: 269-277.
2. Altschul, S.F., W. Gish, W. Miller, E.W. Myers and D.J. Lipman. 1990. Basic local alignment search tool. J Mol Biol., 215: 403-410.
3. Bohs, L. and R.G. Olmstead. 1997. Phylogenetic relationship in Solanum (Solanaceae) based on ndhF sequences. Syst. Botany, 22: 05-17.
4. Chiang, T.Y., B.A. Schaal and C.I. Peng. 1998. Universal primers for amplification and sequencing a noncoding spacer between the atpB and rbcL genes of chloroplast DNA. Bot. Bull. Acad. Sin., 39: 245-250.
5. D'Arcy, W.G. 1979. Classification of Solanaceae. In: The Biology and Taxonomy of the Solanaceae. (Eds.): G.J. Hawkes, R.N. Lester and A.D. Skelding. Academic Press, London, pp 03-47.
6. D'Arcy, W.G. 1991. The Solanaceae since 1976, with a review of its biogeography. In: Solanaceae III: Taxonomy, Chemistry and Evolution. (Eds.): J.G. Hawks, R.N. Lester, M. Nee and N. Eserada. Royal Botanic Garden, Kew and the Linnean Society of London, Richmond, pp 75-137.
7. Dong, W., J. Liu, J. Yu, L. Wang and S. Zhou. 2012 Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS ONE 7: e35071
8. Doyle, J.J. and J.L. Doyle. 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull., 19: 11-15.
9. Ehrendorfer, F, J.F. Manen and A. Natali. 1994. cpDNA intergene sequences corroborate restriction site data for reconstructing Rubiaceae phylogeny. Plant Syst. Evol., 190: 245-258.
10. Farris, J.S. 1989. The retention index and the rescaled consistency index. Cladistics, 5: 417-419.
11. Felsenstain, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39:783-791.
12. Gao, X., Y.P. Zhu, B.C. Wu, Y.M. Zhao, J.Q. Chen and Y.Y. Hang. 2008. Phylogeny of Dioscorea sect. Stenophora based on chloroplast matK, rbcL and trnL-F sequences. J. Syst. Evol., 46: 315-321.
13. Halamova, K., L. Kokoska, Z. Polesny, K. Macakova, J. Flesar and V. Rada. 2013. Selective In vitro growth inhibitory effect of withania somnifera on human pathogenic bacteria and bifidobacteria. Pak. J. Bot., 45: 667-670.
14. Hawkes, J.G. 1992. Biosystematics of the potato. In: The Potato crop. (Ed.): P.M. Harris. Chapman and Hall, London, pp. 909.
15. Hilu, K.W., C. Black, D. Diouf and J.G. Burleigh. 2008. Phylogenetic signal in matK vs. trnK: A case study in early diverging eudicots (angiosperms). Mol. Phylogenet Evol., 48: 1120-1130.
16. Hoot, S.B. and A.W. Douglas. 1998. Phylogeny of the Proteaceae based on atpB and atpB-rbcLintergenic spacer region sequences. Aust Syst Bot., 11: 301-320.
17. Hoot, S.B. and W.C. Taylor. 2001 The utility of nuclear ITS, a LEAFY homolog intron, and chloroplast atpB-rbcL spacer region data in phylogenetic analyses and species delimitation in Isoëtes. Am Fern J., 91:166-177.
18. Hunziker, A.T. 1979. South American Solanaceae: A synoptic survey. In: The Biology and Taxonomy of the Solanaceae. (Eds.): G.J. Hawkes, R.N. Lester and A.D. Skelding. Academic Press, London, pp 49-85.
19. Hunziker, A.T. 2001 Genera Solanacearum: The genera of Solanaceae illustrated, arranged according to a new system. ARG Gantner Verlag KG Ruggell, Germany,pp 500.
20. Hurst, G.D.D. and F.M. Jiggins. 2005 Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proc R Soc B., 272: 1525-1534.
21. Janssensad, S., K. Geutena, Y.M. Yuanb, Y. Songb, P. Küpferb and E. Smetsac. 2006. Phylogenetics of impatiens and Hydrocera (Balsaminaceae) using chloroplast atpB-rbcL Spacer Sequences. Syst. Botany, 31: 171-180.
22. Edmonds, J.M. and J.A. Chweya. 1997. Black nightshades. Solanum nigrum L., and related species. Promoting the conservation and use of underutilized and neglected crops. 15. Institute of Plant Genetics and Crop Plant Research, Gatersleben/International Plant Genetic Resources Institute, Rome, Italy. pp 09.
23. Khan, S., F. Al-Qurainy, M. Nadeem and M. Tarroum. 2013. Selection of chloroplast DNA markers for the development of DNA barcode and reconstruction of phylogeny of senecio asirensis boulos and jri wood. Pak. J. Bot., 45: 703-710.
24. Kim, K.J. and R.K. Jansen. 1995. ndhF sequence evolution and the major clades in the sunflower family. Proc Natl. Acad. Sci. USA., 92: 10379-10383.
25. Kluge, A.G. and J.S. Farries. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool., 18: 1-32.
26. Li, J.H. 2008 Phylogeny of Catalpa (Bignoniaceae) inferred from sequences of chloroplast ndhF and nuclear ribosomal DNA. J. Syst. Evol., 46: 341-348.
27. Manen, J., A. Natali and F. Ehrendorfer. 1994. Phylogeny of Rubiaceae-Rubieae inferred from the sequence of a cpDNA intergenic region. Pl. Syst. Evol., 190: 195-211.
28. Manen, J.F. and A. Natali. 1995. Comparison of the evolution of ribulose-1, 5-biphosphate carboxylase (rbcL) and atpBrbcL noncoding spacer sequences in a recent plant group, the tribe Rubieae (Rubiaceae). J. Mol. Evol., 41: 920-927.
29. Martins, T.R. and T.J. Barkman. 2005 Reconstruction of Solanaceae phylogeny using the nuclear gene SAMT. Syst Botany, 30: 435-447.
30. Nasir, Y.J. 1985. Solanaceae. In: Flora of Pakistan. (Eds.): E. Nasir & S.I. Ali. Pakistan Agricultural Research Council, Islamabad, 168: 1-61.
31. Olmstead, R.G. and JA. Sweere. 1994. Combining data in phylogenetic systematics: An empirical approach using three molecular data sets in the Solanaceae. Syst. Biol., 43: 467-481.
32. Olmstead, R.G. and J.D. Palmer. 1992. A chloroplast DNA phylogeny of the Solanaceae: Subfamilial relationships and character evolution. Ann. Missouri Bot. Gard., 79: 346-360.
33. Olmstead, R.G., J.A. Sweere, R.E. Spangler, L. Bohs and J.D. Palmer. 1999. Phylogeny and provisional classification of the Solanaceae based on chloroplast DNA. In: Solanaceae IV: Advances in Biology and Utilization. (Eds.): M. Nee, D. Symon, R.N. Lester & J. Jessop. Royal Botanic Gardens, Kew, pp. 111-137.
34. Olmstead, R.G., L. Bohs, H.A. Migid, E. Santiago-Valentin, V.F. Garcia and S.M. Collier. 2008. A Molecular Phylogeny of the Solanaceae. Taxon., 57: 1159-1181.
35. Palmer, J.D. 1991. Plastid chromosomes: structure and evolution. In: The molecular biology of plastids (Cell Culture and Somatic Cell Genetics of Plants, (Eds.): L. Bogorad & I.K. Vasil. Vol. 7a. Academic Press, San Diego, pp. 5-53.
36. Peterson, P.M., K. Romaschenko and G. Johnson. 2010. A classification of the Chloridoideae (Poaceae) based on multi-gene phylogenetic trees. Mol. Phylogenet Evol., 55: 580-598.
37. Rozen, S. and H.J. Skaletsky. 1998 Primer 3. Code available at http://www-genome.wi.mit.edu/genome_software/other/ primer3.html.
38. Shinwari, Z.K, R. Terauchi and S. Kawano. 1994. Phylogenetic relationships among genera in the Liliaceae- Asparagoideae-Polygonatae sensu lato inferred from rbcL gene sequence data. PI. Systematic & Evolution., 192: 263-277.
39. Shinwari, Z.K., R. Terauchi and S. Kawano. 1994a Molecular Systematics of Liliaceae-Asparagoideae-Polygonatae. 1. RFLP analysis of cpDNA in several species of Asiatic Disporum species. Plant Species Bio., 9: 11-18.
40. Shinwari, Z.K., R. Terauchi; F.H. Utech and S. Kawano. 1994b. Recognition of the New World Disporum Section Prosartes as Prosartes (Liliaceae) based on the sequence data of the rbcL gene. Taxon, 43(3): 353-366.
41. Shinwari, Z.K. 1995 Congruence between morphology and molecular phylogeneties in Prosartes (Liliaceae). Pak. J. Bot. 27(2): 361-369.
42. Swofford, D.L. 2002 PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0b10.Sinauer Associates, Sunderland, Massachusetts.
43. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22: 4673-4680.
44. Walsh, B.M. and S.H. Hoot. 2001. Phylogenetic relationships of Capsicum (Solanaceae) from two noncoding regions: the chloroplast atpB-rbcL spacer region and nuclear waxy intron. Int. J. Plant Sci., 162: 1409-1418.
45. Wilson, C.A. 2009. Phylogenetic relationships among the recognized series in Iris Section Limniris. Syst Botany, 34: 277-284.
46. Wolfe, K.H., W.H. Li and P.M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc. Natl. Acad. Sci. USA, 84: 9054-9058
47. Wolfe, K.H. and P.M. Sharp. 1988.Identification of functional open reading frames in chloroplast genomes. Gene., 66: 215-222.
48. Yousuf, Z., S. Masood, Z.K. Shinwari, M.A. Khan and A. Rabani. 2006. Evaluation of taxonomic status of medicinal species of the genus Solanum and Capsicum based on polyacrylamide gel electrophoresis. Pak. J. Bot., 38: 99-106.
49. Yousuf, Z., S. Masood, Z.K. Shinwari, M.A. Khan and A. Rabani. 2008. Evaluation of taxonomic status of the medicinal species of the genus Hyoscyamous, Withania,Atropa and Datura based on polyacrylamide gel electrophoresis. Pak. J. Bot., 40: 1827-1833.