Hegarty MJ, Hiscock SJ: Hybrid speciation in plants: new insights from molecular studies. New Phytol. 2005, 165: 411-423.
Article
CAS
PubMed
Google Scholar
Zhang P, Li W, Friebe B, Gill BS: Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH. Genome. 2004, 47: 979-987. 10.1139/g04-042.
Article
CAS
PubMed
Google Scholar
Iwataa H, Katob T, Ohnoc S: Triparental origin of damask roses. Gene. 2000, 259: 53-10.1016/S0378-1119(00)00487-X.
Article
Google Scholar
Lim KY, Werlemark G, Matyasek R, Bringloe JB, Sieber V, El Mokadem H, Meynet J, Hemming J, Leitch AR, Roberts AV: Evolutionary implications of permanent odd polyploidy in the stable sexual, pentaploid of Rosa canina L. Heredity. 2005, 94: 501-506. 10.1038/sj.hdy.6800648.
Article
CAS
PubMed
Google Scholar
Raymond O, Piola F, Sanlaville-Boisson C: Inference of reticulation in outcrossing allopolyploid taxa: caveats, likelihood and perspectives. Trends Ecol Evol. 2002, 17: 3-6. 10.1016/S0169-5347(01)02378-3.
Article
Google Scholar
Puizina J, Javornik B, Bohanec B, Schweizer D, Maluszynska J, Papeš D, Schweizer D: Random amplified polymorphic DNA analysis, genome size, and genomic in situ hybridization of triploid viviparous onions. Genome. 1999, 42: 1208-1216. 10.1139/g99-023.
Article
CAS
PubMed
Google Scholar
Puizina J: Shallots in Croatia – genetics, morphology and nomenclature. Acta Bot Croat. 2013, 72 (2): 387-398.
Google Scholar
Singh F, Ved Brat S, Khoshoo TN: Natural triploidy in viviparous onions. Cytologia. 1967, 32: 403-407. 10.1508/cytologia.32.403.
Article
Google Scholar
Puizina J, Papeš D: Cytogenetical evidence for hybrid structure and origin of diploid and triploid shallots (Allium cepa var. viviparum, Liliaceae) from Dalmatia (Croatia). Plant Syst Evol. 1996, 199: 203-215. 10.1007/BF00984905.
Article
Google Scholar
Maass HI: Studies on triploid viviparous onions and their origin. Genet Resour Crop Ev. 1997, 44: 95-99. 10.1023/A:1008606706218.
Article
Google Scholar
Friesen N, Klaas M: Origin of some minor vegetatively propagated Allium crops studied with RAPD and GISH. Genet Resour Crop Ev. 1998, 45: 511-523. 10.1023/A:1008647700251.
Article
Google Scholar
Klaas M, Friesen N: Molecular markers in Allium. In Allium Crop Science:Recent Advances. Edited by Rabinowitch HD, Currah L. Wallingford OxonOX108DE: CABI Publishing, CAB International; 2001:l5–l31.
Google Scholar
Langer A, Koul AK: Studies on nucleolus and nucleolar chromosomes in angiosperms. VII. Nature of nucleolar chromosome polymorphism in Allium cepa var. viviparum (Metzg.) Alef. Cytologia. 1983, 48: 323-332. 10.1508/cytologia.48.323.
Article
Google Scholar
Puizina J, Papeš D: Further cytogenetic analyses of the Croatian triploid shallot "Ljutika" (Allium cepa var. viviparum, Alliaceae) and its comparison with the Indian triploid "Pran". Plant Syst Evol. 1997, 208: 11-23. 10.1007/BF00986079.
Article
Google Scholar
Visiani R: Flora Dalmatica 1. Lipsiae: Hofmeister; 1842.
Google Scholar
Stearn WT: Allium L. Flora Europea 5. Edited by: Tutin TG, Heywood VH.Cambridge: University Press; 1980.
Google Scholar
Puizina J: Cytogenetic and Molecular Characteristics of Natural Hybrids andPolyploids of Red Onion (Allium cepa L.) PhD. thesis. University of Zagreb,Science Department; 1997.
Google Scholar
Koul AK, Gohil RN: Further studies on natural triploidy in viviparous onions. Cytology. 1971, 36: 253-261. 10.1508/cytologia.36.253.
Article
Google Scholar
Havey MJ: Molecular characterization of the interspecific origin of viviparous onion. J Hered. 1991, 82: 501-503.
CAS
Google Scholar
Havey MJ: Restriction enzyme analysis of the chloroplast and nuclear 45 s ribosomal DNA of Allium sections Cepa and Phyllodolon (Alliaceae). Plant Syst Evol. 1992, 183: 17-31. 10.1007/BF00937732.
Article
CAS
Google Scholar
Havey MJ: A putative donor of S-cytoplasm and its distribution among open-pollinated populations of onion. Theor Appl Genet. 1993, 86: 128-134.
Article
CAS
PubMed
Google Scholar
Gurushidze M, Mashayekhi S, Blattner FR, Friesen N, Fritsch RM: Phylogenetic relationship of wild and cultivated species of Allium section Cepa inferred by nuclear rDNA ITS sequence analysis. Plant Syst Evol. 2007, 269: 259-269. 10.1007/s00606-007-0596-0.
Article
CAS
Google Scholar
Friesen N, Fritsch RM, Blattner FR: Phylogeny and new infrageneric classification of Allium L.(Alliaceae) based on nuclear ribosomal DNA ITS sequences. Aliso. 2006, 22: 372-395.
Google Scholar
Hirschegger P, Jakse J, Trontelj P, Bohanec B: Origins of Allium ampeloprasum 788 horticultural groups and a molecular phylogeny of the section Allium (Allium: 789 Alliaceae). Mol Phylogenet Evol. 2010, 54: 488-497. 10.1016/j.ympev.2009.08.030.
Article
CAS
PubMed
Google Scholar
Li QQ, Zhou SD, He XY, Yu Y, Zhang YC, Wei XQ: Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Ann Bot. 2010, 106 (5): 709-733. 10.1093/aob/mcq177.
Article
PubMed Central
CAS
PubMed
Google Scholar
Guenaoui C, Mang S, Figliuolo G, Neffati M: Diversity in Allium smpheloprasum: from small and wild to large and cultivated. Genet Resour Crop Ev. 2013, 60 (1): 97-114. 10.1007/s10722-012-9819-5.
Article
Google Scholar
Ricroch A, Yockteng R, Brown SC, Nadot S: Evolution of genome size across some cultivated Allium species. Genome. 2005, 48 (3): 511-520. 10.1139/g05-017.
Article
CAS
PubMed
Google Scholar
Son JH, Park KC, Lee AI, Jeon EJ, Kim HH, Kim NS: Sequence variation and comparison of the 5S rRNA sequences in Allium species and their chromosomal distribution in four Allium species. J Plant Biol. 2012, 55: 15-25. 10.1007/s12374-011-9185-4.
Article
CAS
Google Scholar
Shibata F, Hizume M: Evolution of 5S rDNA units and their chromosomal localization in Allium cepa and Allium schoenoprasum revealed by microdissection and FISH. Theor App Genet. 2002, 105: 167-172. 10.1007/s00122-002-0950-0.
Article
CAS
Google Scholar
Baldwin BG: Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the Compositae. Mol Phylogenet Evol. 1992, 1: 3-16. 10.1016/1055-7903(92)90030-K.
Article
CAS
PubMed
Google Scholar
Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF, Campbell CS, Donoghue MJ: The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann Missouri Bot Gard. 1995, 82: 247-277. 10.2307/2399880.
Article
Google Scholar
King RA, Gornall RJ, Preston CD, Croft JM: Molecular confirmation of Potamogeton x bottnicus (P. pectinatus x P. vaginatus, Potamogetonaceae) in Britain. Bot J Linn Soc. 2001, 135: 67-70.
Google Scholar
Liu B, Brubaker CL, Mergeai G, Cronn RC, Wendel JF: Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome. 2001, 44: 321-330. 10.1139/g01-011.
Article
CAS
PubMed
Google Scholar
Muir G, Fleming CC, Schlötterer C: Three divergent rDNA clusters predate the species divergence in Quercus petraea (Matt.) Liebl. and Quercus robur L. Mol Biol Evol. 2001, 18: 112-119. 10.1093/oxfordjournals.molbev.a003785.
Article
CAS
PubMed
Google Scholar
Kaplan Z, Fehrer J: Evidence for the hybrid origin of Potamogeton x cooperi (Potamogetonaceae): traditional morphologybased taxonomy and molecular techniques in concert. Folia Geobot. 2004, 39: 431-453. 10.1007/BF02803212.
Article
Google Scholar
Kovarik A, Pires JC, Leitch AR, Lim KY, Sherwood A, Matyasek R, Rocca J, Soltis DE, Soltis PS: Rapid concerted evolution of nuclear ribosomal DNA in two allopolyploids of recent and recurrent origin. Genetics. 2005, 169: 931-944. 10.1534/genetics.104.032839.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kovarik A, Dadejova M, Lim KY, Chase MW, Clarkson JJ, Knapp S, Leitch AR: Evolution of rDNA in Nicotiana allopolyploids: a potential link between rDNA homogenization and epigenetics. Ann Bot. 2008, 101: 815-823. 10.1093/aob/mcn019.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lim KY, Matyasek R, Kovarik A, Leitch AR: Parental origin and genome evolution in the allopolyploid Iris versicolor. Ann Bot. 2007, 100: 219-224. 10.1093/aob/mcm116.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lim KY, Soltis DE, Soltis PS, Tate J, Matyasek R, Srubarova H, Kovarik A, Pires JC, Xiong Z, Leitch AR: Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS ONE. 2008, 3 (10): e3353-10.1371/journal.pone.0003353.
Article
PubMed Central
PubMed
Google Scholar
Puizina J, Sviben T, Krajačić-Sokol I, Zoldoš-Pećnik V, Šiljak-Yakovlev S, Papeš D, Besendorfer V: Cytogenetic and molecular characterization of Abies alba genome and its relationship with other members of Pinaceae family. Plant Biol. 2008, 10: 256-267. 10.1111/j.1438-8677.2007.00018.x.
Article
CAS
PubMed
Google Scholar
Ksiazczyk T, Kovarik A, Eber F, Huteau V, Khaitova L, Tesarikova Z, Coriton O, Chevre AM: Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploidy species Brassica napus. Chromosoma. 2011, 120: 557-571. 10.1007/s00412-011-0331-z.
Article
CAS
PubMed
Google Scholar
Maluszynska J, Hasterok R, Weiss H: rRNA genes – their distribution andactivity in plants. In Plant Cytogenetics. Edited by Małuszynska J. Katowice:Silesian University Press; 1998:75–95.
Google Scholar
Weiss-Schneeweiss H, Schneeweiss GM: Karyotype diversity andevolutionary trends in angiosperms. In Plant Genome Diversity, Volume 2,Physical Structure, Behavior and Evolution of Plant Genomes. Edited byLeitch IJ, Greilhuber J, Doležel J, Wendel JF. Wien: Springer-Verlag;2013:209–230.
Google Scholar
Alvarez I, Wendel JF: Ribosomal ITS sequences and plant phylogenetic inference. Mol Phylogenet Evol. 2003, 29: 417-434. 10.1016/S1055-7903(03)00208-2.
Article
CAS
PubMed
Google Scholar
Nieto Feliner G, Rosselló JA: Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol. 2007, 44: 911-919. 10.1016/j.ympev.2007.01.013.
Article
CAS
PubMed
Google Scholar
Volkov RA, Medina FJ, Zentgraf U, Hemleben V: Organization and molecular evolution of rDNA, nucleolar dominance, and nucleolus structure. Prog Bot. 2004, 65: 106-146. 10.1007/978-3-642-18819-0_5.
Article
CAS
Google Scholar
Mlinarec J, Šatović Z, Malenica N, Ivančić-Baće I, Besendorfer V: Evolution of the tetraploid Anemone multifida (2n = 32) and hexaploid A. baldensis (2n = 48) (Ranunculaceae) was accompanied by rDNA loci loss and intergenomic translocation: evidence for their common genome origin. Ann Bot. 2012, 110: 703-712. 10.1093/aob/mcs128.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fulneček J, Lim KY, Leitch AR, Kovarik A, Matyašek R: Evolution and structure of 5S rDNA loci in allotetraploid Nicotiana tabacum and its putative parental species. Heredity. 2002, 88: 19-25. 10.1038/sj.hdy.6800001.
Article
PubMed
Google Scholar
Gottlob-McHugh SG, Lévesque M, MacKenzie K, Olson M, Yarosh O, Johnson DA: Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plants. Genome. 1990, 33: 486-494. 10.1139/g90-072.
Article
CAS
PubMed
Google Scholar
Kellogg EA, Appels R: Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics. 1995, 140: 325-343.
PubMed Central
CAS
PubMed
Google Scholar
Besendorfer V, Krajačić-Sokol I, Jelenić S, Puizina J, Mlinarec J, Sviben T, Papeš D: Two classes of 5S rDNA unit arrays of the silver fir, Abies alba Mill.: structure, localization and evolution. Theor Appl Genet. 2005, 110: 730-741. 10.1007/s00122-004-1899-y.
Article
CAS
PubMed
Google Scholar
Lepen I, Puizina J: FISH mapping of 18S-5.8S-26S rRNA genes and flourochorme banding in the triploid viviparous onion Allium x cornutum Clementi ex Visiani, 1842. Acta Biol Cracov Bot. 2011, 53: 111-116.
Google Scholar
Kotseruba V, Pistrick K, Blattner FR, Kumke K, Weiss O, Rutten T, Fuchs J, Endo T, Nasuda S, Ghukasyan A, Houben A: The evolution of the hexaploid grass Zingeria kochii (Mez) Tzvel. (2n = 12) was accompanied by complex hybridization and uniparental loss of ribosomal DNA. Mol Phylogenet Evol. 2010, 56: 146-155. 10.1016/j.ympev.2010.01.003.
Article
PubMed
Google Scholar
Clarkson JJ, Lim KY, Kovarik A, Chase MW, Knapp S, Leitch AR: Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae). New Phytol. 2005, 168: 241-252. 10.1111/j.1469-8137.2005.01480.x.
Article
CAS
PubMed
Google Scholar
Ma XF, Gustafson JP: Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res. 2005, 109: 236-249. 10.1159/000082406.
Article
CAS
PubMed
Google Scholar
Weiss-Schneeweiss H, Schneeweiss GM, Stuessy TF, Mabuchi T, Park JM, Jang CG, Sun BY: Chromosomal stasis in diploids contrasts with genome restructuring in auto- and allopolyploid taxa of Hepatica (Ranunculaceae). New Phytol. 2007, 174: 669-682. 10.1111/j.1469-8137.2007.02019.x.
Article
CAS
PubMed
Google Scholar
Weiss-Schneeweiss H, Tremetsberger K, Schneeweiss GM, Parker JS, Stuessy TF: Karyotype diversification and evolution in diploid and polyploid South American Hypochaeris (Asteraceae) inferred from rDNA localization and genetic fingerprint data. Ann Bot. 2008, 101: 909-918. 10.1093/aob/mcn023.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hizume M: Allodiploid nature of Allium wakegi Araki revealed by genomic in situ hybridization and localization of 5S and 18S rDNAs. Jpn J Genet. 1994, 69: 407-415. 10.1266/jjg.69.407.
Article
CAS
PubMed
Google Scholar
Ricroch A, Peffey EB, Baker RJ: Chromosomal location of rDNA in Allium: in situ hybridization using biotin- and fluorescein-labelled probe. Theor Appl Genet. 1992, 83: 413-418.
Article
CAS
PubMed
Google Scholar
Lee SH, Do GS, Seo BB: Chromosomal localization of 5S rRNA gene loci and implications for relationships within the Allium complex. Chrom Res. 1999, 7: 89-93. 10.1023/A:1009222411001.
Article
CAS
PubMed
Google Scholar
Do GS, Seo BB, Yamamoto M, Suzuki G, Mukai Y: Identification and chromosomal location of tandemly repeated DNA sequences in Allium cepa. Genes Genet Syst. 2001, 76: 53-60. 10.1266/ggs.76.53.
Article
CAS
PubMed
Google Scholar
Saghai Maaroof MA, Soliman KM, Jorgensen RA, Allard RW: Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA. 1984, 81: 8014-8018. 10.1073/pnas.81.24.8014.
Article
Google Scholar
Bezić N, Šamanić I, Dunkić V, Besendorfer V, Puizina J: Essential Oil composition and internal transcribed spacer (ITS) sequence variability of four south-Croatian satureja species (lamiaceae). Molecules. 2009, 14: 925-938. 10.3390/molecules14030925.
Article
PubMed
Google Scholar
Hall TA: BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999, 41: 95-98.
CAS
Google Scholar
Higgins DG, Thompson JD, Gibson TJ: Using CLUSTAL for multiple sequence alignments. Meth Enzymol. 1996, 266: 383-402.
Article
CAS
PubMed
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28: 2731-2739. 10.1093/molbev/msr121.
Article
PubMed Central
CAS
PubMed
Google Scholar
Librado P, Rozas J: DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009, 25: 1451-1452. 10.1093/bioinformatics/btp187.
Article
CAS
PubMed
Google Scholar
Ronquist F, Huelsenbeck JP: MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19: 1572-1574. 10.1093/bioinformatics/btg180.
Article
CAS
PubMed
Google Scholar
Akaike H: A new look at the statistical model identification. IEEE Trans Autom Control. 1974, 19: 716-723. 10.1109/TAC.1974.1100705.
Article
Google Scholar
Posada D: JModelTest: phylogenetic model averaging. Mol Biol Evol. 2008, 25: 1253-1256. 10.1093/molbev/msn083.
Article
CAS
PubMed
Google Scholar
Swofford DL: PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods),Version 4.0b.10 for 32-Bit Microsoft Windows. Sunderland, MA, USA: Sinauer Associates; 2001.
Google Scholar
Gerlach WL, Dyer TA: Sequence organization of the repeating units in the nucleus of wheat which contain 5S rRNA genes. Nucleic Acid Res. 1980, 8: 4851-4865. 10.1093/nar/8.21.4851.
Article
PubMed Central
CAS
PubMed
Google Scholar
Torres-Ruiz RA, Hemleben V: Pattern and degree of methylation in ribosomal RNA genes of Cucurbita pepo L. Plant Mol Biol. 1994, 26: 1167-1179. 10.1007/BF00040697.
Article
CAS
PubMed
Google Scholar
Weiss-Schneeweiss H, Riha K, Jang CG, Puizina J, Scherthan H, Schweizer D: Chromosome termini of the monocot plant Othocallis siberica are maintained by telomerase, which specifically synthesizes vertebrate-type telomere sequences. Plant J. 2004, 37: 484-493. 10.1046/j.1365-313X.2003.01974.x.
Article
CAS
PubMed
Google Scholar