5S Ribosomal DNA of Distantly Related Quercus Species: Molecular Organization and Taxonomic Application

Govaerts, R. and Frodin, D.G., World checklist and bibliography of Fagales, Kew, UK: Royal Botanic Gardens, 1998.

Nixon, K.C., Global and neotropical distribution and diversity of oak (genus Quercus) and oak forests, in Ecology and Conservation of Neotropical Montane Oak Forests, Berlin, Heidelberg: Springer, 2006, pp. 3–13. https://doi.org/10.1007/3-540-28909-7_1

Deng, M., Jiang, X.L., Hipp, A.L., Manos, P.S., and Hahn, M., Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia, Mol. Phylogenet. Evol., 2018, vol. 119, pp. 170–181. https://doi.org/10.1016/j.ympev.2017.11.003

Denk, T. and Grimm, G.W., The oaks of western Eurasia: traditional classifications and evidence from two nuclear markers, Taxon, 2010, vol. 59, no. 2, pp. 351–366. https://doi.org/10.1002/tax.592002

Simeone, M.C., Grimm, G.W., Papini, A., Vessella, F., Cardoni, S., Tordoni, E., Piredda, R., Franc, A., and Denk, T., Plastome data reveal multiple geographic origins of Quercus group Ilex,Peer. J, 2016, vol. 4. e1897. https://doi.org/10.7717/peerj.1897

Denk, T., Grimm, G.W., Manos, P.S., Deng, M., and Hipp, A.L., An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns, in Oaks Physiological Ecology: Exploring the Functional Diversity of Genus Quercus L., Cham: Springer, 2017, pp. 13–38. https://doi.org/10.1007/978-3-319-69099-5_2

Van Valen, L., Ecological species, multispecies, and oaks, Taxon, 1976, vol. 25, nos. 2/3, pp. 233–239. https://doi.org/10.2307/1219444

Hubert, F., Grimm, G.W., Jousselin, E., Berry, V., Franc, A., and Kremer, A., Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus,Syst. Biodivers., 2014, vol. 12, no. 4, pp. 405–423. https://doi.org/10.1080/14772000.2014.941037

Pham, K.K., Hipp, A.L., Manos, P.S., and Cronn, R.C., A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny, Genome, 2017, vol. 60, no. 9, pp. 720–732. https://doi.org/10.1139/gen-2016-0191

McVay, J.D., Hauser, D., Hipp, A.L., and Manos, P.S., Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America, Genome, 2017, vol. 60, no. 9, pp. 733–742. https://doi.org/10.1139/gen-2016-0206

Simeone, M.C., Cardoni, S., Piredda, R., Imperatori, F., Avishai, M., Grimm, G.W., and Denk, T., Comparative systematics and phylogeography of Quercus section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation, Peer J., 2018, vol. 6. e5793. https://doi.org/10.7717/peerj.5793

Hipp, A.L., Manos, P.S., Hahn, M., Avishai, M., Bodénes, C., Cavender-Bares, J., Crowl, A., Deng, M., Denk, T., Fitz-Gibbon, S., Gailing, O., González-Elizondo, M.S., González-Rodríguez, A., Grimm, G.W., Jiang, X-L., Kremer, A., Lesur, I., McVay, J.D., Plomion, C., Rodríguez-Correa, H., Schulze, E-D., Simeone, M.C., Sork, V.L., and Valencia-Avalos, S., Genomic landscape of the global oak phylogeny, bioRxiv, 2019, p. 587253. https://doi.org/10.1101/587253

Barron, E., Averyanova, A., Kvacek, Z., Momohara, A., Pigg, K.B., Popova, S., Postigo-Mijarra, J.M., Tiffney, B.H., Utescher, T., and Zhou, Z.K., The fossil history of Quercus, in Oaks Physiological Ecology: Exploring the Functional Diversity of Genus Quercus L., Cham: Springer, 2017, pp. 39–105. https://doi.org/10.1007/978-3-319-69099-5_3

Chengjiu, H., Yongtian, Z., and Bartholomew, B., Fagaceae, in Flora of China, Zheng-Yi, W. and Raven, P., Eds., Beijing: Science Press, 1999, vol. 4, pp. 300–400.

Grant, V., Plant Speciation, New York: Columbia Univ. Press, 1981, 2nd ed.

Soltis, P.S. and Soltis, D.E., The role of hybridization in plant speciation, Ann. Rev. Plant Biol., 2009, vol. 60, pp. 561–588. https://doi.org/10.1146/annurev.arplant.043008.092039

Volkov, R.A., Medina, F.J., Zentgraf, U., and Hemleben, V., Molecular cell biology: organization and molecular evolution of rDNA, nucleolar dominance, and nucleolus structure, Progr. Bot., 2004, vol. 65, pp. 106–146. https://doi.org/10.1007/978-3-642-18819-0_5

Volkov, R.A., Zanke, C., Panchuk, I.I., and Hemleben, V., Molecular evolution of 5S rDNA of Solanum species (sect. Petota): application for molecular phylogeny and breeding, Theor. Appl. Genet., 2001, vol. 103, no. 8, pp. 1273–1282. https://doi.org/10.1007/s001220100670

Saini, A. and Jawali, N., Molecular evolution of 5S rDNA region in Vigna subgenus Ceratotropis and its phylogenetic implications, Plant Syst. Evol., 2009, vol. 280, nos. 3–4, p. 187. https://doi.org/10.1007/s00606-009-0178-4

Calio, M.F., Lepis, K.B., Pirani, J.R., and Struwe, L., Phylogeny of Helieae (Gentianaceae): Resolving taxonomic chaos in a Neotropical clade, Mol. Phylogenet. Evol., 2017, vol. 106, pp. 192–208. https://doi.org/10.1016/j.ympev.2016.09.013

Porebski, S., Bailey, L.G., and Baum, B.R., Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components, Plant Mol. Biol. Rep., 1997, vol. 15, no. 1, pp. 8–15. https://doi.org/10.1007/BF02772108

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J., Basic local alignment search tool, J. Mol. Biol., 1990, vol. 215, no. 3, pp. 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

Thompson, J.D., Higgins, D.G., and Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 1994, vol. 22, no. 22, pp. 4673–4680. https://doi.org/10.1093/nar/22.22.4673

Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 2004, vol. 32, no. 5, pp. 1792–1797. https://doi.org/10.1093/nar/gkh340

Stamatakis, A., RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 2014, vol. 30, no. 9, pp. 1312–1313. https://doi.org/10.1093/bioinformatics/btu033

Sork, V.L., Squire, K., Gugger, P.F., Steele, S.E., Levy, E.D., and Eckert, A.J., Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata,Am. J. Bot., 2016, vol. 103, no. 1, pp. 33–46. https://doi.org/10.1007/s11295-016-0975-1

Tynkevich, Y.O. and Volkov, R.A., Structural organization of 5S ribosomal DNA in Rosa rugosa,Cytol. Genet., 2014, vol. 48, no. 1, pp. 3–9. https://doi.org/10.3103/S0095452714010095

Tynkevich, Y.O., Nevelska, A.O., Chorney, I.I., and Volkov, R.A., Organization and variability of the 5S rDNA intergenic spacer of Lathyrus venetus,Bull. Vavilov Soc. Genet. Breed. Ukr., 2015, vol. 13, no. 1, pp. 81–87.

Rusak, O.O., Petrashchuk, V.I., Panchuk, I.I., and Volkov, R.A., Molecular organization of 5S rDNA in two Ukrainian populations of Sycamore (Acer pseudoplatanus), Bull. Vavilov Soc. Genet. Breed. Ukr., 2016, vol. 14, no. 2, pp. 216–220.

Shelyfist, A.Y., Tynkevich, Y.O., and Volkov, R.A., Molecular organization of 5S rDNA of Brunfelsia uniflora (Pohl.) D. Don., Bull. Vavilov Soc. Genet. Breed. Ukr., 2018, vol. 16, no. 1, pp. 61–68.

Douet, J. and Tourmente, S., Transcription of the 5S rRNA heterochromatic genes is epigenetically controlled in Arabidopsis thaliana and Xenopus laevis,Heredity, 2007, vol. 99, pp. 5–13. https://doi.org/10.1038/sj.hdy.6800964

Simon, L., Rabanal, F.A., Dubos, T., Oliver, C., Lauber, D., Poulet, A., Vogt, A., and Mandlbauer, A., Le Goff S., Sommer A., Duborjal H., Tatout C., and Probst, A.V., Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana,Nucleic Acids Res., 2018, vol. 46, no. 6, pp. 3019–3033. https://doi.org/10.1093/nar/gky163

Volkov, R.A., Panchuk, I.I., Borisjuk, N.V., Hosiawa-Baranska, M., Maluszynska, J., and Hemleben, V., Evolutional dynamics of 45S and 5S ribosomal DNA in ancient allohexaploid Atropa belladonna,BMC Plant Biol., 2017, vol. 17, no. 1, pp. 1–15. https://doi.org/10.1186/s12870-017-0978-6

Ishchenko, O.O., Panchuk, I.I., Andreev, I.O., Kunakh, V.A., and Volkov, R.A., Molecular organization of 5S ribosomal DNA of Deschapmpsia antarctica,Cytol. Genet., 2018, vol. 52, no. 6, pp. 416–421. https://doi.org/10.3103/S0095452719010146

Volkov, A.R. and Panchuk, I.I., 5S rDNA of Dactylus glomerata (Poaceae): molecular organization and taxonomic application, Bull. Vavilov Soc. Genet. Breed. Ukr., 2014, vol. 12, no. 1, pp. 3–11.

Ishchenko, O.O. and Panchuk, I.I., Molecular organization of 5S rDNA of perennial ryegrass Lolium perenne L., Bull. Vavilov Soc. Genet. Breed. Ukr., 2018, vol. 16, no. 2, pp. 166–173.

Garcia, S., Panero, J.L., Siroky, J., and Kovarik, A., Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family, BMC Plant Biol., 2010, vol. 10, no. 1, pp. 176. https://doi.org/10.1186/1471-2229-10-176

Tamayo-Ordonez, Y.J., Narváez-Zapata, J.A., Tamayo-Ordonez, M.C., and Sánchez-Teyer, L.F., Retroelements and DNA methylation could contribute to diversity of 5S rDNA in Agave L., J. Mol. Evol., 2018, vol. 86, no. 6, pp. 404–423. https://doi.org/10.1007/s00239-018-9856-6

Ribeiro, T., Loureiro, J., Santos, C., and Morais-Cecilio, L., Evolution of rDNA FISH patterns in the Fagaceae, Tree Genet. Genomes, 2011, vol. 7, no. 6, pp. 1113–1122. https://doi.org/10.1007/s11295-011-0399