Abstract
Chloroplast intergenic psbA-trnH spacer has recently become a popular tool in plant molecular phylogenetic studies at low taxonomic level and as suitable for DNA barcoding studies. In present work, we studied the organization of psbA-trnH in the large family Umbelliferae and its potential as a DNA barcode and phylogenetic marker in this family. Organization of the spacer in Umbelliferae is consistent with a general pattern evident for angiosperms. The 5′-region of the spacer situated directly after the psbA gene is more conserved in length compared to the 3′-region, which has greater sequence variation. This pattern can be attributed to the maintenance of the secondary structural elements in the 5′-region of the spacer needed for posttranscriptional regulation of psbA gene expression. In Umbelliferae only, the conserved region contains a duplication of the fragment corresponding to the loop of the stem-loop structure and an independent appearance of identical sequence complementarities (traits) necessary to stabilize the stem-loop structure in different lineages. The 3′-region of the spacer nearest to trnH ranges greatly in size, mainly due to deletions, and the decrease in spacer length is a general trend in the evolution psbA-trnH in Umbelliferae. The features revealed in spacer organization allow us to use it as phylogenetic marker, and indels seem to be more informative for analyses than nucleotide substitutions. However, high conservation among closely related taxa and occurrence of homoplastic inversions in the stem-loop structure limit its application as DNA barcode.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Schneier, V. S. (2005) Botan. Zh., 90, 3–18.
Antonov, A. S. (2006) Genosystematics of Plants [in Russian], Akademkniga, Moscow.
Hebert, P. D. N., Cywinska, A., Ball, S. L., and deWaard, J. R. (2003) Proc. R. Soc. Lond. B, 270, 313–321.
Chase, M. W., Salamin, N., Wilkinson, M., Dunwell, J. M., Kesanakurthi, R. P., Haidar, N., and Savolainen, V. (2005) Phil. Trans. R. Soc. B, 360, 1889–1895.
Cowan, R. S., Chase, M. W., Kress, W. J., and Savolainen, V. (2006) Taxon, 55, 611–616.
Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A., and Janzen, D. H. (2005) Proc. Natl. Acad. Sci. USA, 102, 8369–8374.
Brown, G. K., Nelson, G., and Ladiges, P. Y. (2006) J. Biogeogr., 33, 1929–1944.
Miikeda, O., Koichi, K., Handa, T., and Yukawa, T. (2006) Bot. J. Linn. Soc., 152, 153–168.
Kulcheski, F. R., Muschner, V. C., Lorenz-Lemke, A. P., Stehmann, J. R., Bonatto, S. L., Salzano, F. M., and Freitas, L. B. (2006) Genetica, 126, 3–14.
Yao, H, Song, J. Y., Ma, X. Y., Liu, C., Li, Y., Xu, H. X., Han, J. P., Duan, L. S., and Chen, S. L. (2009) Planta Med., 75, 667–669.
Newmaster, S. G., Fazekas, A. J., Steeves, R. A. D., and Janovec, J. (2008) Mol. Ecol. Resour., 8, 480–490.
Nicolas, A. N., and Plunkett, G. M. (2009) Mol. Phylogenet. Evol., 53, 134–151.
Downie, S. R., Spalik, K., Katz-Downie, D. S., and Reduron, J.-P. (2010) Pl. Div. Evol., 128, 111–136.
Logacheva, M. D., Valiejo-Roman, C. M., and Pimenov, M. G. (2008) Pl. Syst. Evol., 270, 139–157.
Degtjareva, G. V., Kljuykov, E. V., Samigullin, T. H., Valiejo-Roman, C. M., and Pimenov, M. G. (2009) Bot. J. Linn. Soc., 160, 149–170.
Valiejo-Roman, C. M., Terentieva, E. I., Pimenov, M. G., Kljuykov, E. V., Samigullin, T. H., and Tilney, P. M. (2012) Syst. Bot., 37, 573–581.
Edgar, R. C. (2004) BMC Bioinformatics, 5, 113.
Hall, T. A. (1999) Nucleic Acids Symp. Ser., 41, 95–98.
Leontovich, A. M., Brodsky, L. I., and Gorbalenya, A. E. (1993) Biosystems, 30, 57–63.
Zuker, M. (2003) Nucleic Acids Res., 31, 3406–3415.
De Rijk, P., and van de Peer, Y. (1997) Nucleic Acids Res., 25, 117–122.
Storchova, H., and Olson, M. S. (2007) Pl. Syst. Evol., 268, 235–256.
Wilson, K. S., and von Hippel, P. H. (1995) Proc. Natl. Acad. Sci. USA, 92, 8793–8797.
Stern, D. B., and Gruissem, W. (1987) Cell, 51, 1145–1157.
Stern, D. B., Jones, H., and Gruissem, W. (1989) J. Biol. Chem., 264, 18742–18750.
Nickelsen, J., and Link, G. (1990) Mol. Gen. Genet., 228, 89–96.
Tonkyn, J. C., and Gruissem, W. (1993) Mol. Gen. Genet., 241, 141–152.
Singer, M., and Berg, P. (1998) Genes and Genomes [Russian translation], Vol. 2, Mir, Moscow.
Stern, D. B., Radwanski, E. R., and Kindle, K. L. (1991) Plant Cell, 3, 285–297.
Adams, C. C., and Stern, D. B. (1990) Nucleic Acids Res., 25, 6003–6010.
Kelchner, S. A., and Wendel, J. F. (1996) Curr. Genet., 30, 259–262.
Kelchner, S. A. (2000) Ann. Missouri Bot. Gard., 87, 482–498.
Quandt, D., Muller, K., and Huttunen, S. (2003) Pl. Biol., 5, 400–410.
Whitlock, B. A., Hale, A. M., and Groff, P. A. (2010) PLoS One, 5, e11533.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © G. V. Degtjareva, M. D. Logacheva, T. H. Samigullin, E. I. Terentieva, C. M. Valiejo-Roman, 2012, published in Biokhimiya, 2012, Vol. 77, No. 9, pp. 1273–1283.
Rights and permissions
About this article
Cite this article
Degtjareva, G.V., Logacheva, M.D., Samigullin, T.H. et al. Organization of chloroplast psbA-trnH intergenic spacer in dicotyledonous angiosperms of the family umbelliferae. Biochemistry Moscow 77, 1056–1064 (2012). https://doi.org/10.1134/S0006297912090131
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006297912090131