Phylogenetic analysis of selected representatives of the genus Erica based on the genes encoding the DNA-dependent RNA polymerase I

Angelika Maria Gomolińska 1 , Monika Szczecińska 1 , Jakub Sawicki 1 , 2 , Katarzyna Krawczyk 1 ,  and Piotr Szkudlarz 3
  • 1 Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, 10-727, Olsztyn, Poland
  • 2 Department of Biology and Ecology, University of Ostrava, Ostrava
  • 3 Department of Plant Taxonomy, Adam Mickiewicz University, 61-614, Poznań, Poland


The rpo genes are characterized by rapidly-evolving sequences. They encode subunits of plastid-encoded (PEP) polymerase (rpoA, rpoB, rpoC1 and rpoC2). This polymerase is one of the most important enzymes in the chloroplasts. The primary aim of the research was to study the rate of molecular evolution in the rpo genes and to estimate these genes as phylogenetic markers based on the example of the genus Erica (Ericaceae). The tested rpo genes demonstrated similarities on multiple levels, for example: phylogenetic informativeness, variation level, intragenic mutation rates and the effect of intragenic mutations on the properties of encoded peptides. This study did not confirm that the analyzed rpo genes are reliable markers and may be helpful in understanding phylogenetic relationships between species that belong to the same genus. The rpoC2 gene was found to be a most useful phylogenetic marker in the Erica genus, while rpoC1 was found to be the least promising gene.

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • Allison L. A., Simon L. D. & Maliga P. 1996. Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO Journal 15: 2802-2809.

  • Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J. & Wheeler D. L. 2005. GenBank. Nucleic Acids Research. 40: 34-38.

  • Bentham G. 1839. Ericaceae. In A. P. De Candolle, Prodromus systematis naturalis regni vegetabilis, 7: 580-733. Treutel & Weiss, Paris.

  • Blazier J. C., Ruhlman T. A., Weng M. L., Rehman S. K., Sabir J. S. M. & Jansen R. K. 2016. Divergence of RNA polymerase α subunits in angiosperm plastid genomes is mediated by genomic rearrangement. Scientific Reports. DOI: 10.1038/srep24595

  • Botanical Garden in Kew website. Available online: (accessed on 21 January 2017).

  • Britton T., Anderson C. L., Jacquet D., Lundqvist S. & Bremer K. 2007. Estimating divergence times in large phylogenetic trees. Systematic Biology. 56: 741–752.

  • Bruzone M. C., Fontenla S. B. & Vohník M. 2015. Is the prominent ericoid mycorrhizal fungus Rhizoscyphus ericae absent in the Southern Hemisphere’s Ericaceae? A case study on the diversity of root mycobionts in Gaultheria spp. From northwest Patagonia, Argentina. Mycorrhiza 25(1): 25-40. DOI 10.1007/s00572-014-0586-3

  • Chelo I. M., Zé-Zé L. & Tenreiro R. 2007. Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK. International Journal of Systematic and Evolutionary Microbiology 57: 276-286.

  • Chotewutmontri P. & Barkan A. 2016. Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize. PLoS Genet 12 (7): e1006106. doi:10.1371/journal.pgen.1006106

  • Christelová P., Valárik M., Hřibová E., de Langhe E. & Doležel J. 2011. A multi-gene sequence-based phylogeny of the Musaceae (banana) family. BMC Evolutionary Biology. 11:103. doi: 10.1186/1471-2148-11-103

  • Darriba D., Taboada G. L., Doallo R. & Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8): 772.

  • Edgar R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-97.

  • Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.

  • Fig Tree, version 1.4.2. Software for molecular evolution, phylogenetics and epidemiology. Available online: (accessed on 29 January 2017).

  • Gillespie E. & Kron K. 2010. Molecular phylogenic relationships and a revised classification of the subfamily Ericoidae (Ericaceae). Molecular Phylogenetics and Evolution 56: 343-354.

  • Glen H. F. 2002. Cultivated Plants of Southern Africa. 428 pp. Jacana, Johannesburg.

  • Hall T. A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nuclear Acids Symposium Series 41: 95-98.

  • Hansen I. 1950. Die europäischen Arten der Gattung Erica L. Bot. Jarhb. 75: 1-81.

  • Hulsenbeck J. P. & Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.

  • Jeffroy O., Brinkmann H., Delsuc F. & Philippe H. 2006. Phylogenomics: The beginning of incongruence? Trends in Genetics 22: 225-231.

  • Korczak B., Christensen H., Emler S., Frey J. & Kuhnert P. 2004. Phylogeny of the family Pasteurellaceae based on rpoB sequences. International Journal of Systematic and Evolutionary Microbiology 54: 1393-1399.

  • Krause K., Falk J., Humbeck K. & Krupinska K. 1998. Responses of the transcriptional apparatus of barley chloroplasts to a prolonged dark period and to subsequent re-illumination. Journal of Plant Physiology 104: 143-152.

  • Krawczyk K. & Sawicki J. 2013. The Uneven Rate of the Molecular Evolution of Gene Sequences of DNA-Dependent RNA Polymerase I of the Genus Lamium L. International Journal of Molecular Science 14: 11376-11391.

  • Liere K., Weihe A. & Borner T. 2011. The transcription machineries of plant mitochondria and chloroplasts: composition, function and regulation. Journal of Plant Physiology 168: 1345-1360.

  • Linder H. P. 2003. The radiation of the Cape flora, southern Africa. Biological Review. 78: 597-638.

  • L P. & Goldman N. 1998. Models of molecular evolution and phylogeny. Genome Research 8: 1233-1244.

  • Little M. C. & Hallick R. B. 1988. Chloroplast rpoA, rpoB, and rpoC genes specify at least three components of a chloroplast DNA-dependent RNA polymerase active in tRNA and mRNA transcription. Journal of Biological Chemistry 263: 14302-14307.

  • Logacheva M. D., Penin A. A., Samigullin T. H., Vallejo-Roman C. M. & Antonov A. S. 2007. Phylogeny of flowering plants by the chloroplast genome sequences: In search of a “Lucky Gene”. Biochemistry 72: 1324-1330.

  • Lopez-Giraldez F. & Townsend J. P. 2011. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evolutionary Biology. doi:10.1186/1471-2148-11-152.

  • Maddison W. P. & Knowles L. L. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematical Biology 55: 21-30.

  • Mayrose I., Graur D., Ben-Tal N. & Pupko T. 2004. Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior. Molecular Biology and Evolution 21: 1781-1791

  • Mcguire A. F. & Kron K. A. 2005. Phylogenetic relationships of European and African Ericas. International Journal of Plant Science 166: 311-318.

  • Nei M. & Kumar S. 2000. Molecular Evolution and Phylogenetics. xiv+333 pp. Oxford University Press, New York, NY, USA.

  • Newmaster S. G, Fazekas A. J, Steeves R. A. D. & Janovec J. 2008. Testing candidate plant barcode regions in the Myristicaceae. Molecular Ecology Research 8: 480-490.

  • Ojeda F., Budde K. B. & Heuertz M. 2015. Biogeography and evolution of seeder and resprouter forms of Erica coccinea (Ericaceae) in the fire-prone Cape fynbos. Plant Ecology. DOI: 10.1007/s11258-015-0539-8.

  • Oliver E. G. H. 1993. Studies in the Ericoideae (Ericaceae). XI. The generic relationship between Erica and Blaeria. Kew Bulletin 48: 771-780.

  • Oliver E. G. H. 2000. Systematics of Ericeae (Ericaceae: Ericoideae): species with indehiscent and partially dehiscent fruits. Contributions from the Bolus Her-barium 19: 1-483.

  • Oliver E. G. H. 1993. Studies in the Ericoideae (Ericaceae). XII. The placing of the genus Blaeria into synonymy under Erica; nomenclatural and taxonomic changes for the southern African region. Bothalia 23: 1-7.

  • Oliver E. G. H. & Oliver I. M. 2003. Ericaceae. In: G. Germishuizen & N. L. Meyer (eds.). Plants of southern Africa: an annotated checklist, pp 424-451. Strelitzia. National Botanical Institute, Pretoria.

  • Petersen G. & Seberg O. 1997. Phylogenetic analysis of the Triticeae (Poaceae) based on rpoA sequence data. Molecular Phylogenetics and Evolution 7: 217-230.

  • Pirie M. D., Oliver E. G. H. & Bellstedt D. U. 2011. A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggest numerous shifts in floral macro-morphology. Molecular Phylogenetics and Evolution 61: 593-601.

  • Posada D. 2008. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256.

  • Pond S. L. K. & Muse S. V. 2005. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21: 676-679.

  • Schumann D., Kirsten G. & Oliver E. G. H. 1992. Ericas of South Africa. 272 pp. Fernwood Press, Cape Town.

  • Serino G. & Maliga P. 1998. RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme. Plant Physiology 117: 1165-1170.

  • Stevens P. F., Luteyn J., Oliver E. G. H., Bell T. L., Brown E. A., Crowden R. K., George A. S., Jordan G. J., Ladd P., Lemson K., Mcclean C. B., Menadue Y., Pate J. S., Stace H. M. & Weiller C. M. 2004. Ericaceae. In: K. Kubitzki (ed.). The Families and Genera of Vascular Plants, pp. 145-194. Springer-Verlad, Berlin-Heidelberg New York.

  • Szczecińska M., Gomolińska A., Szkudlarz P. & Sawicki J. 2014. Plastid and nuclear genomic resources of a relict and endangered plant species: Chamaedaphne calyculata (L.) Moench (Ericaceae). Turkish Journal of Botany 38: 1229-1238.

  • Tamura K., Stecher G., Peterson D., Filipski A. & Kumar S. 2013. MEGA 6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution 30: 2725-2729.

  • Townsend J. P. 2007. Profiling phylogenetic informativeness. Systematic Biology 56: 222-231.

  • Townsend J. P., López-Giráldez F. & Friedman R. 2008. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. Journal Molecular of Systematic and Evolution 67: 437-447.

  • Townsend J. P. & Leuenberger C. 2011. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Systematic Biology 60: 358-365.

  • Woolley S., Johnson J., Smith M. J., Crandall K. A. & Mcclellan D. A. 2003. TreeSAAP: Selection on amino acid properties using phylogenetic trees. Bioinformatics 19: 671-672.

  • Xia X. & Xie Z. 2001. DAMBE: Software package for data analysis in molecular biology and evolution. Journal of Heredity 92: 371-373.

  • Xia X. 2013. DAMBE 5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution. Molecular Biology and Evolution 30(7): 1720-1728.

  • Yagi Y. & Shiina T. 2014. Recent advances in the study of chloroplast gene expression and its evolution. Front Plant Science 5: 61-68.

  • Yang Z. 1996. Among site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11: 367-372.

  • Yoichi W. & Tomaru N. 2014. Patterns of geographic distribution have a considerable influence on population genetic structure in one common and two rare species of Rhododendron (Ericaceae). Tree Genetics & Genomes 10: 827-837.


Journal + Issues