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

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: 2802-2809.10.1002/j.1460-2075.1996.tb00640.xOpen DOISearch in Google Scholar

Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J. & Wheeler D. L. 2005. GenBank. Nucleic Acids Research. 40: 34-38.10.1093/nar/gkj157134751916381837Search in Google Scholar

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

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/srep2459510.1038/srep24595483455027087667Open DOISearch in Google Scholar

Botanical Garden in Kew website. Available online: http://www.kew.org/barcoding/protocols/ (accessed on 21 January 2017).Search in Google Scholar

Britton T., Anderson C. L., Jacquet D., Lundqvist S. & Bremer K. 2007. Estimating divergence times in large phylogenetic trees. Systematic Biology. 56: 741–752.10.1080/1063515070161378317886144Search in Google Scholar

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/s00572-014-0586-310.1007/s00572-014-0586-324838300Open DOISearch in Google Scholar

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: 276-286.10.1099/ijs.0.64468-017267964Open DOISearch in Google Scholar

Chotewutmontri P. & Barkan A. 2016. Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize. PLoS Genet 12 (7): e1006106. doi:10.1371/journal.pgen.100610610.1371/journal.pgen.1006106494509627414025Search in Google Scholar

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: 10.1186/1471-2148-11-10310.1186/1471-2148-11-103310262821496296Open DOISearch in Google Scholar

Darriba D., Taboada G. L., Doallo R. & Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9(8): 772.10.1038/nmeth.2109459475622847109Search in Google Scholar

Edgar R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-97.10.1093/nar/gkh34039033715034147Search in Google Scholar

Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.10.1111/j.1558-5646.1985.tb00420.x28561359Search in Google Scholar

Fig Tree, version 1.4.2. Software for molecular evolution, phylogenetics and epidemiology. Available online: http://tree.bio.ed.ac.uk/software/figtree/ (accessed on 29 January 2017).Search in Google Scholar

Gillespie E. & Kron K. 2010. Molecular phylogenic relationships and a revised classification of the subfamily Ericoidae (Ericaceae). Molecular Phylogenetics and Evolution 56: 343-354.10.1016/j.ympev.2010.02.02820193767Open DOISearch in Google Scholar

Glen H. F. 2002. Cultivated Plants of Southern Africa. 428 pp. Jacana, Johannesburg.Search in Google Scholar

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.Search in Google Scholar

Hansen I. 1950. Die europäischen Arten der Gattung Erica L. Bot. Jarhb. 75: 1-81.Search in Google Scholar

Hulsenbeck J. P. & Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.10.1093/bioinformatics/17.8.75411524383Open DOISearch in Google Scholar

Jeffroy O., Brinkmann H., Delsuc F. & Philippe H. 2006. Phylogenomics: The beginning of incongruence? Trends in Genetics 22: 225-231.10.1016/j.tig.2006.02.00316490279Open DOISearch in Google Scholar

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: 1393-1399.10.1099/ijs.0.03043-015280320Search in Google Scholar

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: 143-152.10.1034/j.1399-3054.1998.1040201.xSearch in Google Scholar

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: 11376-11391.10.3390/ijms140611376370973723759988Search in Google Scholar

Liere K., Weihe A. & Borner T. 2011. The transcription machineries of plant mitochondria and chloroplasts: composition, function and regulation. Journal of Plant Physiology 168: 1345-1360.10.1016/j.jplph.2011.01.005Search in Google Scholar

Linder H. P. 2003. The radiation of the Cape flora, southern Africa. Biological Review. 78: 597-638.10.1017/S1464793103006171Search in Google Scholar

Lió P. & Goldman N. 1998. Models of molecular evolution and phylogeny. Genome Research 8: 1233-1244.10.1101/gr.8.12.12339872979Search in Google Scholar

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: 14302-14307.10.1016/S0021-9258(18)68221-3Search in Google Scholar

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: 1324-1330.10.1134/S0006297907120061Search in Google Scholar

Lopez-Giraldez F. & Townsend J. P. 2011. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evolutionary Biology. doi:10.1186/1471-2148-11-152.10.1186/1471-2148-11-152312442821627831Open DOISearch in Google Scholar

Maddison W. P. & Knowles L. L. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematical Biology 55: 21-30.10.1080/1063515050035492816507521Search in Google Scholar

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: 1781-179110.1093/molbev/msh19415201400Open DOISearch in Google Scholar

Mcguire A. F. & Kron K. A. 2005. Phylogenetic relationships of European and African Ericas. International Journal of Plant Science 166: 311-318.10.1086/427478Search in Google Scholar

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

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: 480-490.10.1111/j.1471-8286.2007.02002.x21585825Search in Google Scholar

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/s11258-015-0539-8.10.1007/s11258-015-0539-8Open DOISearch in Google Scholar

Oliver E. G. H. 1993. Studies in the Ericoideae (Ericaceae). XI. The generic relationship between Erica and Blaeria. Kew Bulletin 48: 771-780.10.2307/4118856Search in Google Scholar

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.Search in Google Scholar

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: 1-7.10.4102/abc.v23i1.779Search in Google Scholar

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.Search in Google Scholar

Petersen G. & Seberg O. 1997. Phylogenetic analysis of the Triticeae (Poaceae) based on rpoA sequence data. Molecular Phylogenetics and Evolution 7: 217-230.10.1006/mpev.1996.03899126564Open DOISearch in Google Scholar

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: 593-601.10.1016/j.ympev.2011.06.00721722743Open DOISearch in Google Scholar

Posada D. 2008. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256.10.1093/molbev/msn08318397919Open DOISearch in Google Scholar

Pond S. L. K. & Muse S. V. 2005. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21: 676-679.10.1093/bioinformatics/bti07915509596Open DOISearch in Google Scholar

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

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: 1165-1170.10.1104/pp.117.4.1165348809701572Search in Google Scholar

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.10.1007/978-3-662-07257-8_19Search in Google Scholar

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: 1229-1238.10.3906/bot-1405-80Open DOISearch in Google Scholar

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: 2725-2729.10.1093/molbev/mst197384031224132122Search in Google Scholar

Townsend J. P. 2007. Profiling phylogenetic informativeness. Systematic Biology 56: 222-231.10.1080/1063515070131136217464879Search in Google Scholar

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: 437-447.10.1007/s00239-008-9142-018696029Search in Google Scholar

Townsend J. P. & Leuenberger C. 2011. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Systematic Biology 60: 358-365.10.1093/sysbio/syq09721303824Search in Google Scholar

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: 671-672.10.1093/bioinformatics/btg04312651734Open DOISearch in Google Scholar

Xia X. & Xie Z. 2001. DAMBE: Software package for data analysis in molecular biology and evolution. Journal of Heredity 92: 371-373.10.1093/jhered/92.4.37111535656Search in Google Scholar

Xia X. 2013. DAMBE 5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution. Molecular Biology and Evolution 30(7): 1720-1728.10.1093/molbev/mst064Open DOISearch in Google Scholar

Yagi Y. & Shiina T. 2014. Recent advances in the study of chloroplast gene expression and its evolution. Front Plant Science 5: 61-68.10.3389/fpls.2014.00061Search in Google Scholar

Yang Z. 1996. Among site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11: 367-372.10.1016/0169-5347(96)10041-0Open DOISearch in Google Scholar

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: 827-837.10.1007/s11295-014-0723-3Search in Google Scholar