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Oak ribosomal DNA: characterization by FISH and polymorphism assessed by IGS PCR–RFLP

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Abstract

Oaks taxonomy has been revised over the years, demanding expeditious and cost-effective tools for DNA fingerprinting and taxonomic discrimination. We focused on the characterization of the ribosomal DNA (rDNA) of 22 Quercus species, belonging to four infrageneric groups, using silver nitrate staining, fluorescence in situ hybridization (FISH) and IGS PCR–RFLP markers (produced by the digestion of the rDNA intergenic spacer, IGS). A chromosome complement of 2n = 2x = 24 was confirmed in 21 species, and ascribed to Quercus phellos. Silver nitrate staining detected one or two nucleoli per nucleus, and two nucleolar organizer regions (NORs) per prometaphase cells. FISH performed with rDNA probes revealed two 5S and four 35S rDNA loci in nine species and confirmed their location in the remaining. Since no cytogenetic polymorphisms were detected, the IGS was studied. A single amplicon with ca. 2 kb was amplified in all oaks, and digested with six restriction enzymes, that produced a total of 125 IGS PCR–RFLP fragments with 99.2 % of polymorphism. A monomorphic HaeIII fragment with 225 bp was found. Among the infrageneric groups, 11 monomorphic bands were observed and 6 were considered group-specific. Based on the pool of molecular data different genetic analyses were performed. The UPGMA dendrogram clustered most of the oaks per infrageneric group, and was corroborated by the principal coordinates analysis (PCoA). The genetic structure also matched the assumed taxonomy. Globally, IGS PCR–RFLP proved their usefulness for DNA fingerprinting, evaluation of phylogenies and genetic structure, proving to be an adequate complementary tool for rDNA based studies in genus Quercus.

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References

  • Appels R, Dvořák J (1982) The wheat ribosomal DNA spacer region: its structure and variation in populations and among species. Theor Appl Genet 63:337–348

    Article  CAS  PubMed  Google Scholar 

  • Bacchetta G (2001) Números cromosomáticos de plantas occidentales. Anales Jard Bot Madrid 58:341–342

    Google Scholar 

  • Bauer N, Horvat T, Birus I, Vicic V, Zoldos V (2009) Nucleotide sequence, structural organization and length heterogeneity of ribosomal DNA intergenic spacer in Quercus petraea (Matt.) Liebl. and Q. robur L. Molec Genet Genomics 281:207–221

    Article  CAS  Google Scholar 

  • Belahbib N, Pemonge MH, Ouassou A, Sbay H, Kremer A, Petit RJ (2001) Frequent cytoplasmic exchanges between oak species that are not closely related: Quercus suber and Q. ilex in Morocco. Molec Ecol 10:2003–2012

    Article  CAS  Google Scholar 

  • Bellarosa R (2003) Brief synthesis of the current knowledge on cork oak. In: Varela MC (ed.) Handbook of the EU concerted action on cork oak, FAIR I CT 95 0202, INIA, Lisbon, pp 11–22

  • Bellarosa R, Delre V, Schirone B, Maggin F (1990) Ribosomal RNA genes in Quercus spp. (Fagaceae). Pl Syst Evol 172:127–139

    Article  CAS  Google Scholar 

  • Bellarosa R, Simeone MC, Papini A, Schirone B (2005) Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp. Molec Phylogen Evol 34:355–370

    Article  CAS  Google Scholar 

  • Bik HM, Fournier D, Sung W, Bergeron RD, Thomas WK (2013) Intra-genomic variation in the ribosomal repeats of nematodes. PLOS One 8(10):e78230. doi:10.1371/journal.pone.0078230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Butorina AK (1993) Cytogenetic study of diploid and spontaneous triploid oaks Quercus robur L. Ann Forest Sci 50(1):144s–150s

    Article  Google Scholar 

  • Byung-Yun S, Park JH, Kwak MJ, Kim CH, Kim KS (1996) Chromosome counts from the flora of Korea with emphasis on Apiaceae. J Pl Biol 39:15–22

    Google Scholar 

  • Cao M, Zhou ZK (2000) A karyotype analysis of nine species of the Quercus from China. Guihaia 20:341–345

    Google Scholar 

  • Carvalho A, Paula A, Guedes-Pinto H, Martins L, Carvalho J, Lima-Brito J (2009) Preliminary genetic approach based on both cytogenetic and molecular characterizations of nine oak species. Pl Biosyst 143:S25–S33

    Article  Google Scholar 

  • Carvalho A, Polanco C, Lima-Brito J, Guedes-Pinto H (2010) Differential rRNA genes expression in hexaploid wheat related to NOR Methylation. Pl Molec Biol Reporter 28:403–412

    Article  CAS  Google Scholar 

  • Carvalho A, Guedes-Pinto H, Lima-Brito J (2011) Intergenic spacer length variants in Old Portuguese bread wheat cultivars. J Genet 90:203–208

    Article  PubMed  Google Scholar 

  • Chokchaichamnankit P, Chulalaksananukul W, Phengklai C, Anamthawat-Jónsson K (2007) Karyotypes of some species of Castanopsis, Lithocarpus and Quercus (Fagaceae) from Khun Mae Kuong Forest in Chiang Mai province, Northern Thailand. Thai Forest Bull, Bot 35:38–44

    Google Scholar 

  • Chokchaichamnankit P, Anamthawat-Jónsson K, Chulalaksananukul W (2008) Chromosomal mapping of 18S-25S and 5S ribosomal genes on 15 species of Fagaceae from Northern Thailand. Silvae Genet 57:5–13

    Google Scholar 

  • Chuang JH, Li H (2004) Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLOS Biol 2(2):0253–0263. doi:10.1371/journal.pbio.0020029

    Article  CAS  Google Scholar 

  • Conte L, Cotti C, Cristofolini G (2007) Molecular evidence for hybrid origin of Quercus crenata Lam. (Fagaceae) from Q. cerris L. and Q. suber L. Pl Biosyst 141:181–193

    Article  Google Scholar 

  • Coutinho JP, Carvalho A, Lima-Brito J (2014) Genetic diversity assessment and estimation of phylogenetic relationships among 26 Fagaceae species using ISSRs. Biochem Syst Ecol 54:247–256

    Article  CAS  Google Scholar 

  • Coutinho JP, Carvalho A, Lima-Brito J (2015) Taxonomic and ecological discrimination of Fagaceae species based on internal transcribed spacer polymerase chain reaction - restriction fragment length polymorphism. AoB PLANTS 7:plu079. doi:10.1093/aobpla/plu079

    Google Scholar 

  • Cox AV, Bennett MD, Dyer TA (1992) Use of the polymerase chain reaction to detect spacer size heterogeneity in plant 5S-rRNA gene clusters and to locate such clusters in wheat (Triticum aestivum L.). Theor Appl Genet 83:684–690

    CAS  PubMed  Google Scholar 

  • Dadejová M, Lim KY, Souckova-Skalicka K, Matyasek R, Grandbastien MA, Leitch A, Kovarik A (2007) Transcription activity of rRNA genes correlates with a tendency towards intergenomic homogenization in Nicotiana allotetraploids. New Phytol 174:658–668

    Article  PubMed  Google Scholar 

  • D’Emerico S, Bianco P, Medagli P, Schivone B (1995) Karyotype analysis in Quercus spp. (Fagaceae). Silvae Genet 44:66–70

    Google Scholar 

  • D’Emerico S, Paciolla C, Tommasi F (2000) Contribution to the karyomorphology of some species of the genus Quercus. Silvae Genet 49:243–245

    Google Scholar 

  • Denk T, Grimm GW (2009) Significance of pollen characteristics for infrageneric classification and phylogeny in Quercus (Fagaceae). Int J Pl Sci 170:926–940

    Article  Google Scholar 

  • Denk T, Grimm GW (2010) The oaks of western Eurasia: traditional classifications and evidence from two nuclear markers. Taxon 59:351–366

    Google Scholar 

  • Denk T, Grimm G, Stögerer K, Langer M, Hemleben V (2002) The evolutionary history of Fagus in western Eurasia: evidence from genes, morphology and the fossil record. Pl Syst Evol 232:213–236

    Article  Google Scholar 

  • Denk T, Grímsson F, Zetter R (2010) Episodic migration of oaks to Iceland: evidence for a North Atlantic “Land Bridge” in the latest Miocene. Amer J Bot 97:276–287

    Article  Google Scholar 

  • Denk T, Grímsson F, Zetter R (2012) Fagaceae from the early Oligocene of Central Europe: persisting new world and emerging old world biogeographic links. Rev Palaeobot Palynol 169:7–20

    Article  Google Scholar 

  • Dover GA (1982) Molecular drive: a cohesive mode of species evolution. Nature 299:111–116

    Article  CAS  PubMed  Google Scholar 

  • Dover GA (1989) Linkage disequilibrium and molecular drive in the rDNA gene family. Genetics 122:249–252

    CAS  PubMed  PubMed Central  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull Bot Soc Amer 19:11–15

    Google Scholar 

  • Du FG, Liu JS, Wei ZY, Jin DC (1995) Karyotype analysis of Quercus gilliana Rehd et Wils. J Yanbian Agric Coll 17:208–210

    Google Scholar 

  • Dzialuk A, Chybicki I, Welc M, Sliwinska E, Burczyk J (2007) Presence of triploids among oak species. Ann Bot (Oxford) 99:959–964

    Article  Google Scholar 

  • Flores-Maya S, Flores-Moreno I, Romero-Rangel S, Rojas-Zenteno C, Rubio-Licona LE (2006) Análisis cariológico de ocho especies de encinos (Quercus, Fagaceae) en México. Anales Jard Bot Madrid 63:245–250

    Google Scholar 

  • Ganley ARD, Kobayashi T (2007) Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res 17:184–191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia S, Kovarik A (2013) Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation. Heredity 111:23–33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia S, Garnatje T, Hidalgo O, McArthur ED, Siljak-Yakovlev S, Vallès J (2007) Extensive ribosomal DNA (18S-5.8S-26S and 5S) colocalization in the North American endemic sagebrushes (subgenus Tridentatae, Artemisia, Asteraceae) revealed by FISH. Pl Syst Evol 267:79–92

    Article  CAS  Google Scholar 

  • Garcia S, Panero JL, Siroky J, Kovarik A (2010) Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family. BMC Pl Biol 10:176

    Article  Google Scholar 

  • Garcia S, Garnatje T, Kovarik A (2012) Plant rDNA database: ribosomal DNA loci information goes online. Chromosoma 121:389–394. Release 2.0. Available at: http://www.plantrdnadatabase.com. Accessed 6 May 2015

  • Gerlach WL, Bedbrook JR (1979) Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucl Acids Res 7:1869–1885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gerlach WL, Dyer TA (1980) Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes. Nucl Acids Res 8:4851–4865

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gömöry D, Yakovlev Y, Zhelev P, Jedináková J, Paule L (2001) Genetic differentiation of oak populations within the Quercus robur/Quercus petraea complex in Central and Eastern Europe. Heredity 86:557–563

    Article  PubMed  Google Scholar 

  • Hernández-Vital CR, Alvárez-Moctezuma JG, Zavala-Chávez F, Espinosa-Robles P (2009) Estudio cariológico de Quercus laurina Humb. & Bonpl. Revista Ciencia Forestal en México 34:173–184

    Google Scholar 

  • Hönig K, Riefler M, Kottke I (2000) Survey of Paxillus involutus (Batsch) Fr. inoculum and fruitbodies in a nursery by IGS-RFLPs and IGS sequences. Mycorrhiza 9:315–322

    Article  Google Scholar 

  • Horjales M, Redondo N, Blanco A, Rodríguez MA (2003) Cantidades de DNA nuclear en árboles y arbustos. Nova Acta Científica Compostelana (Bioloxía) 13:23–33

    Google Scholar 

  • Inácio V, Rocheta M, Morais-Cecílio L (2014) Molecular organization of the 25S-18S rDNA IGS of Fagus sylvatica and Quercus suber: a comparative analysis. PLOS One 9(6):e98678. doi:10.1371/journal.pone.0098678

    Article  PubMed  PubMed Central  Google Scholar 

  • Jelesko JG, Carter K, Thompson W, Kinoshita Y, Gruissem W (2004) Meiotic recombination between paralogous RBCSB genes on sister chromatids of Arabidopsis thaliana. Genetics 166:947–957

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jordan EG, Martini G, Bennett MD, Flavell RB (1982) Nucleolar fusion in wheat. J Cell Sci 56:485–495

    Google Scholar 

  • Karvonen P, Savolainen O (1993) Variation and inheritance of ribosomal DNA in Pinus sylvestris L. (Scots pine). Heredity 71:614–622

    Article  CAS  Google Scholar 

  • Kim HJ, Choi YK, Min BR (2001) Variation of the Intergenic Spacer (IGS) Region of Ribosomal DNA among Fusarium oxysporum formae specials. J Microbiol 39:265–272

    CAS  Google Scholar 

  • Kovarik A, Dadejová M, Yoong KL, Chase MW, Clarkson JJ, Knapp S, Leitch AR (2008) Evolution of rDNA in Nicotiana allopolyploids: a potential link between rDNA homogenization and epigenetic. Ann Bot (Oxford) 101:815–823

    Article  CAS  Google Scholar 

  • Kwei-Duan C, Shao-An F, Fang-Chi C, Mei-Chu C (2010) Chromosomal conservation and sequence diversity of ribosomal RNA genes of two distant Oryza species. Genomics 96:181–190

    Article  Google Scholar 

  • Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:281–398

    Google Scholar 

  • Lim KY, Skalicka K, Koukalova B, Volkov RA, Matyasek R, Hemleben V, Leitch AR, Kovarik A (2004) Dynamic changes in the distribution of a satellite homologous to intergenic 26-18S rDNA spacer in the evolution of Nicotiana. Genetics 166:1935–1946

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lima-Brito J, Guedes-Pinto H, Heslop-Harrison JS (1998) The activity of nucleolar organizing chromosomes in multigeneric F1 hybrids involving wheat, triticale, and tritordeum. Genome 41:763–768

    Article  Google Scholar 

  • Lima-de-Faria A (1976) The chromosome field. I-Prediction of the location of ribosomal cistrons. Hereditas (Beijing) 83:1–22

    Article  Google Scholar 

  • Liu YQ, Wang LM, Li MX (1984) Karyotype analysis of eight species of Quercus in Beijing. J Beijing Forest Coll 4:9–15

    Google Scholar 

  • Löve A, Löve D (1982) Reports. In: A. Löve (ed.) IOPB Chromosome number reports, LXXIV, Taxon 31:120–126

  • Maggini F, Baldassini S (1995) Ribosomal RNA genes in the genus Pinus. I. Caryologia 48:17–25

    Article  Google Scholar 

  • Manos PS, Doyle JJ, Nixon KC (1999) Phylogeny, biogeography, and processes of molecular differentiation in Quercus Subgenus Quercus (Fagaceae). Molec Phylogen Evol 12:333–349

    Article  CAS  Google Scholar 

  • Manos PS, Zhe-Kun Z, Cannon CH (2001) Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. Int J Pl Sci 162:1361–1379

    Article  Google Scholar 

  • Martín FG, Beato TA, Anta AS (1999) Estudio cariológico de algunas especies de Quercus (subgen. Quercus) en la Cordillera Cantábrica (España). Stud Bot Univ Salamanca 18:39–46

    Google Scholar 

  • Mateos M, Markow TA (2005) Ribosomal intergenic spacer (IGS) length variation across the Drosophilinae (Diptera: Drosophilidae). BMC Evol Biol 5:46. doi:10.1186/1471-2148-5-46

    Article  PubMed  PubMed Central  Google Scholar 

  • Mayol M, Rosselló JA (2001) Why nuclear ribosomal DNA spacers (ITS) tell different stories in Quercus. Molec Phylogen Evol 19:167–176

    Article  CAS  Google Scholar 

  • Melgarejo P, Martínez JJ, Hernández F, Martínez R, Legua P, Oncina R, Martínez-Murcia A (2009) Cultivar identification using 18S-28S rDNA intergenic spacer-RFLP in pomegranate (Punica granatum L.). Sci Hort (Amsterdam) 120:500–503

    Article  CAS  Google Scholar 

  • Muir G, Fleming CC, Schlötterer C (2001) Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Molec Biol Evol 18:112–119

    Article  CAS  PubMed  Google Scholar 

  • Mukai Y, Endo TR, Gill BS (1990) Physical mapping of the 5S rRNA multigene family in common wheat. J Heredity 81:290–295

    CAS  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individual. Genetics 89:583–590

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nixon KC (1993) Infrageneric classification of Quercus (Fagaceae) and typification of sectional names. Ann Forest Sci 50:25S–34S

    Article  Google Scholar 

  • Ohri D, Ahuja MR (1990) Giemsa C-banded karyotypes in Quercus L (oak). Silvae Genet 39:216–219

    Google Scholar 

  • Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Computer Applic Biosci 12:357–358

    CAS  Google Scholar 

  • Petit RJ, Bodénès C, Ducousso A, Roussel G, Kremer A (2003) Hybridization as a mechanism of invasion in oaks. New Phytol 161:151–164

    Article  Google Scholar 

  • Poczai P, Hyvönen J (2010) Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Molec Biol Rep 37:1897–1912

    Article  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pritchard JK, Wen X, Falush D (2010) Documentation for structure software: version 2.3. University of Chicago, Chicago. Available at: http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_doc.pdf. Accessed 5 March 2015

  • Quirós M, Martorell P, Valderrama MJ, Querol A, Peinado JM, Silóniz MI (2006) PCR-RFLP analysis of the IGS region of rDNA: a useful tool for the practical discrimination between species of the genus Debaryomyces. Antonie van Leeuwenhoek J Microbiol Serol 90:211–219

    Article  Google Scholar 

  • Raina SN, Mukai Y (1999) Detection of a variable number of 18S–5.8S–26S and 5S ribosomal DNA loci by fluorescence in situ hybridization in diploid and tetraploid Arachis species. Genome 42:52–59

    Article  CAS  Google Scholar 

  • Reed KM, Hackett JD, Phillips RB (2000) Comparative analysis of intra-individual and inter-species DNA sequence variation in salmonid ribosomal DNA cistrons. Gene 249:115–125

    Article  CAS  PubMed  Google Scholar 

  • Ribeiro T, Loureiro J, Santos C, Morais-Cecílio L (2011) Evolution of rDNA FISH patterns in the Fagaceae. Tree Genet Genomes 7:1113–1122

    Article  Google Scholar 

  • Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose I (2014) The Chromosome Counts Database (CCDB)– a community resource of plant chromosome numbers. New Phytol 206:19–26. Available at: http://ccdb.tau.ac.il. Accessed 6 May 2015

  • Roa F, Guerra M (2012) Distribution of 35S rDNA sites in chromosomes of plants: structural and evolutionary implications. BMC Evol Biol 12:225. doi:10.1186/1471-2148-12-225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rodriguez TS, Spellenberg R (1992) Chromosome numbers for five Chihuahuan species of Quercus (Fagaceae). Phytologia 72:40–41

    Article  Google Scholar 

  • Rogers SO, Bendich AJ (1987) Ribosomal RNA genes in plants: variability in copy number and in the intergenic spacer. Pl Molec Biol 9:509–520

    Article  CAS  Google Scholar 

  • Rohlf FJ (1998) NTSYS-pc ver. 2.02. Numerical taxonomy and multivariate analysis system. Exeter Publishing, Setauket, USA

  • Ryu S, Do Y, Fitch DHA, Kim W, Mishra B (2008) Dropout alignment allows homology recognition and evolutionary analysis of rDNA intergenic spacers. J Molec Evol 66:368–383

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Molec Biol Evol 4(4):406–425

    CAS  PubMed  Google Scholar 

  • Sanderson SC, Goodrich S, McArthur ED (1984) Asteraceae, Chenopodiaceae, Fagaceae. In: Löve A (ed.) IOPB Chromosome number reports, LXXXV, Taxon 33:756–760

  • Sandhu PS, Mann SK (1988) SOCGI plant chromosome number reports VII. J Cytol Genet 23:219–228

    Google Scholar 

  • Schwarzacher T, Heslop-Harrison JS (2000) Practical in situ hybridization. BIOS Scientific, Oxford

    Google Scholar 

  • Si-Chong C, Cannon CH, Chai-Shian K, Jia-Jia L, Galbraith DW (2014) Genome size variation in the Fagaceae and its implications for trees. Tree Genet Genomes 10:977–988

    Article  Google Scholar 

  • Sneath PHA, Sokal RR (1973) Numerical Taxonomy. Freeman, San Francisco

    Google Scholar 

  • Stack S, Herikhoff L, Sherman J, Anderson L (1991) Staining plant cells with silver. I. The salt nylon technique. Biotechnic Histochem 1:69–78

    Article  CAS  Google Scholar 

  • Tabandeh A, Tabari M, Nodoushan HM, Espahbodi K, Asadicorom F (2012) Karyotypic analysis on Quercus castaneifolia of North of Iran. Iranian J Rangeland Forests Pl Breed Genet Res 20:226–239

    Google Scholar 

  • Taketa S, Ando H, Takeda K, von Bothmer R (2001) Physical locations of 5S and 18S–25S rDNA in Asian and American diploid Hordeum species with the I genome. Heredity 86:522–530

    Article  CAS  PubMed  Google Scholar 

  • Taylor RL, Taylor S (1977) Chromosome numbers of vascular plants of British Columbia. Syesis 10:125–138

    Google Scholar 

  • Thiers B (2010) Index Herbariorum: a global directory of public herbaria and associated staff. New York botanical garden’s virtual herbarium. Available at: http://sweetgum.nybg.org/. Accessed 6 May 2015

  • Váchová M (1978) Reports. In: Májovský J et al. (eds.) Index of chromosome numbers of the Slovakian flora—Part 6. Acta Fac Rerum Nat Univ Comenianae Bot 26:1–42

  • Valbuena-Carabaña M, González-Martínez SC, Sork VL, Collada C, Soto A, Goicoechea PG, Gil L (2005) Gene flow and hybridisation in a mixed oak forest (Quercus pyrenaica Willd. and Quercus petraea (Matts.) Liebl.) in Central Spain. Heredity 95:457–465

    Article  PubMed  Google Scholar 

  • Wang LM (1986) A taxonomic study of the deciduous oaks in China by means of cluster and karyotype analysis. Bull Bot Res Harbin 6:55–69

    Google Scholar 

  • Yap IV, Nelson RJ (1996) Winboot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. International Rice Research Institute (IRRI), Manila, Philippines

    Google Scholar 

  • Yeh FC, Yang RC, Boyle TBJ, Ye ZH, Mao JX (1999) POPGENE version 1.32, the user-friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton USA

  • Yılmaz A, Emel U, Mehmet TB (2008) Karyological studies on four Quercus L. species in Turkey. Caryologia 61:394–401

    Google Scholar 

  • Yılmaz A, Emel U, Mehmet TB (2011) Cytogenetic studies on Quercus L. (Fagaceae) species belonging to Ilex and Cerris section in Turkey. Caryologia 64:297–301

    Article  Google Scholar 

  • Zapatero MAG, Elena-Roselló JÁ, Andrés FN (1988) Números cromosómicos para la flora Española. 504–515. Lagascalia 15:112–119

    Google Scholar 

  • Zoldos V, Pape D, Brown SC, Panaud O, iljak-Yakovlev s (1998) Genome size and base composition of seven Quercus species: inter- and intra-population variation. Genome 41:162–168

    Article  CAS  Google Scholar 

  • Zoldos V, Papes D, Cerbah M, Panaud O, Besendorfer V, Siljak-Yakovlev S (1999) Molecular-cytogenetic studies of ribosomal genes and heterochromatin reveal conserved genome organization among 11 Quercus species. Theor Appl Genet 99:969–977

    Article  CAS  Google Scholar 

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Acknowledgments

J.P.C. acknowledges to the Portuguese Foundation for Science and Technology (Fundação para a Ciência e a Tecnologia, FCT) by his Ph.D. grant SFRH/BD/42837/2008, co-financed by the Fundo Social Europeu/ Programa Operacional Potencial Humano - Quadro de Referência Estratégica Nacional (FSE/POPH-QREN). The authors are very grateful to the Botanical Gardens, listed in Table 1, for providing the seeds used in this work.

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Authors and Affiliations

  1. BioISI-Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, C8 BDG Campo Grande, Lisbon, Portugal

    João P. Coutinho, Ana Carvalho & José Lima-Brito

  2. CSIC-Consejo Superior de Investigáciones Científicas, Cordoba, Spain

    Antonio Martín

  3. Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal

    Teresa Ribeiro & Leonor Morais-Cecílio

  4. Department of Genetics and Biotechnology, University of Tras-os-Montes and Alto Douro, 5001-801, Vila Real, Portugal

    José Lima-Brito

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  1. João P. Coutinho
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Correspondence to José Lima-Brito.

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Funding

This study was funded by the Portuguese Foundation for Science and Technology (Fundação para a Ciência e a Tecnologia, FCT), co-financed by the Fundo Social Europeu/Programa Operacional Potencial Humano—Quadro de Referência Estratégica Nacional (FSE/POPH-QREN), by the attribution of a Ph.D. Grant (SFRH/BD/42837/2008) to the author J.P.C.

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The authors declare that they have no conflict of interest.

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Handling editor: Martin Lysak.

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606_2016_1281_MOESM1_ESM.pdf

List of the known first published studies for 116 Quercus species that reported the number of rDNA loci and the chromosome complement determined by classic cytogenetics or FISH. The table assembles data gathered from: (1) previous studies; (2) the Plant rDNA database (Garcia et al. 2012); and (3) The Chromosome Counts Database (Rice et al. 2014). Species included in this work are presented in bold. (PDF 135 kb)

606_2016_1281_MOESM2_ESM.pdf

IGS PCR–RFLP patterns achieved per species with each restriction enzyme. Species are listed in alphabetic order within the respective infrageneric group. Fragments size presented in base pairs (bp). Infrageneric group-specific (but not unique polymorphic) bands are underlined. (PDF 100 kb)

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Principal coordinates analysis (PCoA) calculated with the pool data gathered with the six restriction enzymes. The plot contains 46 % of the total variation. Species from the same infrageneric group are shown in the same colour. (PDF 256 kb)

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Unrooted phenogram based on the pool of IGS PCR–RFLP data, estimated with POPGENE and visualized with the software TreeView. (PDF 453 kb)

Information on Electronic Supplementary Material

Information on Electronic Supplementary Material

Online Resource 1. List of the known first published studies for 116 Quercus species that reported the number of rDNA loci and the chromosome complement determined by classic cytogenetics or FISH.

Online Resource 2. IGS PCR–RFLP patterns achieved per species with each restriction enzyme.

Online Resource 3. Principal coordinates analysis (PCoA) calculated with the pool data gathered with the six restriction enzymes.

Online Resource 4. Unrooted phenogram based on the pool of IGS PCR–RFLP data, estimated with POPGENE and visualized with the software TreeView.

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Coutinho, J.P., Carvalho, A., Martín, A. et al. Oak ribosomal DNA: characterization by FISH and polymorphism assessed by IGS PCR–RFLP. Plant Syst Evol 302, 527–544 (2016). https://doi.org/10.1007/s00606-016-1281-y

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  • DOI: https://doi.org/10.1007/s00606-016-1281-y

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