View More View Less
  • 1 Council of Scientific and Industrial Research Plant Biotechnology Division, Indian Institute of Integrative Medicine Canal Road Jammu 180 001 India
Restricted access

By employing in silico tools, we devised new chloroplast microsatellite primers for inferring phylogenetic relationships within Brassicaceae. Microsatellite repeats were scanned in 12 chloroplast genomes of Brassicaceae, regions flanking these repeats were aligned and 19 universal primers were designed. Fifteen of these primer pairs are predicted to yield polymorphic amplicons, that are more or less evenly distributed throughout the chloroplast genomes. Finally, using PCR, we have validated three primer pairs on a limited ‘test set’ of plants, different from those used in computational analysis.

  • Angioi, S. A., Desiderio, F., Rau, D., Bitocchi, E., Attene, G., Papa, R. (2009) Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes. Plant Biol (Stuttg) 11, 598–612.

    Papa R. , 'Development and use of chloroplast microsatellites in Phaseolus spp. and other legumes ' (2009 ) 11 Plant Biol (Stuttg) : 598 -612.

    • Search Google Scholar
  • Beilstein, M. A., Al-Shehbaz, I. A., Kellogg, E. A. (2006) Brassicaceae: Phylogeny and trichome evolution. Am. J. Botany 93, 607–619.

    Kellogg E. A. , 'Brassicaceae: Phylogeny and trichome evolution ' (2006 ) 93 Am. J. Botany : 607 -619.

    • Search Google Scholar
  • Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Wheeler, D. L. (2006) GenBank. Nucleic Acids Res. 34, D16–20.

    Wheeler D. L. , 'GenBank ' (2006 ) 34 Nucleic Acids Res. : D16 -20.

  • Carver, T., Thomson, N., Bleasby, A., Berriman, M., Parkhill, J. (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25, 119–120.

    Parkhill J. , 'DNAPlotter: circular and linear interactive genome visualization ' (2009 ) 25 Bioinformatics : 119 -120.

    • Search Google Scholar
  • Cheng, Y., de Vicente, M. C., Meng, H., Guo, W., Tao, N., Deng, X. (2005) A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera. Tree Physiol. 25, 661–672.

    Deng X. , 'A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera ' (2005 ) 25 Tree Physiol. : 661 -672.

    • Search Google Scholar
  • Clegg, M. T., Gaut, B. S., Learn, G. H., Jr., Morton, B. R. (1994) Rates and patterns of chloroplast DNA evolution. Proc. Natl Acad. Sci. USA, 91, 6795–6801.

    Morton B. R. , 'Rates and patterns of chloroplast DNA evolution ' (1994 ) 91 Proc. Natl Acad. Sci. USA : 6795 -6801.

    • Search Google Scholar
  • Couvreur, T. L., Franzke, A., Al-Shehbaz, I. A., Bakker, F. T., Koch, M. A., Mummenhoff, K. (2010) Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Mol. Biol. Evol. 27, 55–71.

    Mummenhoff K. , 'Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae) ' (2010 ) 27 Mol. Biol. Evol. : 55 -71.

    • Search Google Scholar
  • Grant, J. R., Stothard, P. (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 36, W181–184.

    Stothard P. , 'The CGView Server: a comparative genomics tool for circular genomes ' (2008 ) 36 Nucleic Acids Res. : W181 -184.

    • Search Google Scholar
  • He, G., Meng, R., Newman, M., Gao, G., Pittman, R. N., Prakash, C. S. (2003) Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol. 3, 3.

    Prakash C. S. , 'Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.) ' (2003 ) 3 BMC Plant Biol. : 3 -.

    • Search Google Scholar
  • Hong, C. P., Piao, Z. Y., Kang, T. W., Batley, J., Yang, T. J., Hur, Y. K., Bhak, J., Park, B. S., Edwards, D., Lim, Y. P. (2007) Genomic distribution of simple sequence repeats in Brassica rapa. Mol. Cells 23, 349–356.

    Lim Y. P. , 'Genomic distribution of simple sequence repeats in Brassica rapa ' (2007 ) 23 Mol. Cells : 349 -356.

    • Search Google Scholar
  • Katti, M. V., Sami-Subbu, R., Ranjekar, P. K., Gupta, V. S. (2000) Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications. Protein Sci. 9, 1203–1209.

    Gupta V. S. , 'Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications ' (2000 ) 9 Protein Sci. : 1203 -1209.

    • Search Google Scholar
  • Koch, M. A., Mummenhoff, K. (2006) Editorial: Evolution and phylogeny of the Brassicaceae. Plant Syst. Evol. 259, 81–83.

    Mummenhoff K. , 'Editorial: Evolution and phylogeny of the Brassicaceae ' (2006 ) 259 Plant Syst. Evol. : 81 -83.

    • Search Google Scholar
  • Li, Y. C., Korol, A. B., Fahima, T., Beiles, A., Nevo, E. (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 11, 2453–2465.

    Nevo E. , 'Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review ' (2002 ) 11 Mol. Ecol. : 2453 -2465.

    • Search Google Scholar
  • Powell, W., Morgante, M., McDevitt, R., Vendramin, G. G., Rafalski, J. A. (1995) Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of Pines. Proc. Natl Acad. Sci. USA, 92, 7759–7763.

    Rafalski J. A. , 'Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of Pines ' (1995 ) 92 Proc. Natl Acad. Sci. USA : 7759 -7763.

    • Search Google Scholar
  • Provan, J., Biss, P. M., McMeel, D., Mathews, S. (2004). Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae). Mol. Ecol. Notes 4, 262–264.

    Mathews S. , 'Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae) ' (2004 ) 4 Mol. Ecol. Notes : 262 -264.

    • Search Google Scholar
  • Rajendrakumar, P., Biswal, A. K., Balachandran, S. M., Srinivasarao, K., Sundaram, R. M. (2007) Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics 23, 1–4.

    Sundaram R. M. , 'Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions ' (2007 ) 23 Bioinformatics : 1 -4.

    • Search Google Scholar
  • Rajendrakumar, P., Biswal, A. K., Balachandran, S. M., Sundaram, R. M. (2008) In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships. In Silico Biol. 8, 87–104.

    Sundaram R. M. , 'In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships ' (2008 ) 8 In Silico Biol. : 87 -104.

    • Search Google Scholar
  • Rozen, S., Skaletsky, H. (2000) Primer3 on the www for general users and for biologist programmers. Methods Mol. Biol. 132, 365–386.

    Skaletsky H. , 'Primer3 on the www for general users and for biologist programmers ' (2000 ) 132 Methods Mol. Biol. : 365 -386.

    • Search Google Scholar
  • Scheen, A. C., Elven, R., Brochmann, C. (2002) A molecular-morphological approach solves taxonomic controversy in arctic Draba (Brassicaceae). Canadian Journal of Botany 80, 59–71.

    Brochmann C. , 'A molecular-morphological approach solves taxonomic controversy in arctic Draba (Brassicaceae) ' (2002 ) 80 Canadian Journal of Botany : 59 -71.

    • Search Google Scholar
  • Stothard, P., Wishart, D. S. (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21, 537–539.

    Wishart D. S. , 'Circular genome visualization and exploration using CGView ' (2005 ) 21 Bioinformatics : 537 -539.

    • Search Google Scholar
  • Vendramin, G. G., Lelli, L., Rossi, P., Morgante, M. (1996) A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Mol. Ecol. 5, 595–598.

    Morgante M. , 'A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae ' (1996 ) 5 Mol. Ecol. : 595 -598.

    • Search Google Scholar
  • Weising, K., Gardner, R. C. (1999) A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42, 9–19.

    Gardner R. C. , 'A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms ' (1999 ) 42 Genome : 9 -19.

    • Search Google Scholar
  • Zardoya, R., Vollmer, D. M., Craddock, C., Streelman, J. T., Karl, S., Meyer, A. (1996) Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes). Proc. Biol. Sci. 263, 1589–1598.

    Meyer A. , 'Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes) ' (1996 ) 263 Proc. Biol. Sci. : 1589 -1598.

    • Search Google Scholar