Long EO, Dawid IB. Repeated genes in eukaryotes. Annu Rev Biochem. 1980;9:727–64.
Article
Google Scholar
Appels R, Gerlach WL, Dennis ES, Swift H, Peacock WJ. Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals. Chromosoma. 1980;78:293–311.
Article
CAS
Google Scholar
Ellis TN, Lee D, Thomas CM, Simpson PR, Cleary WG, Newman MA, Burcham KWG. 5S rRNA genes in pisum: sequence, long range and chromosomal organization. Mol Gen Genet. 1988;214:333–42.
Article
CAS
PubMed
Google Scholar
Dvorak J, Zhang HB, Kota RS, Lassner M. Organization and evolution of the 5S ribosomal RNA gene family in wheat and related species. Genome. 1989;32:1003–16.
Article
CAS
Google Scholar
Kota RS, Dvorak J. Mapping of a chromosome pairing gene and 5SrRNA genes in Triticum aestivum L. by a spontaneous deletion in chromosome arm 5Bp. Can J Genet Cytol. 1986;28:266–71.
Article
CAS
Google Scholar
Reddy P, Appels R. A second locus for the 5S multigene family in Secale L.: sequence divergence in two lineages of the family. Genome. 1989;32(3):457–67.
Article
CAS
PubMed
Google Scholar
Mukai Y, Endo TR, Gill BS. Physical mapping of the 5S rDNA multigene family in common wheat. J Hered. 1990;81:290–5.
Article
CAS
Google Scholar
Baum BR, Bailey LG. The molecular diversity of the 5S rRNA gene in Kengyilia alatavica (Drobov) J.L. Yang, yen and Baum (Poaceae: Triticeae): potential genomic assignment of different rDNA units. Genome. 1997;40:215–28.
Article
CAS
PubMed
Google Scholar
Baum BR, Johnson DA, Bailey LG. Analysis of 5S rDNA units in the Triticeae: the potential to assign sequence units to haplomes. In: Jaradat AA, editor. Triticeae III, science publishers inc. New Hampshire: Enfield; 1998. p. 85–96.
Google Scholar
Baum BR, Bailey LG. The 5S rRNA gene sequence variation in wheats and polyploid wheat progenitors, and the information it conveys about genome constitution in Triticum L. (Poaceae: Triticeae). Genetic Res Crop Evol. 2001;48:35–51.
Article
Google Scholar
Baum BR, Bailey LG, Belyayev A, Raskina O, Nevo E. The utility of the non-transcribed spacer of the 5S rDNA units grouped into unit classes assigned to haplomes – test on cultivated wheat and wheat progenitors. Genome. 2004;47:590–9.
Article
CAS
PubMed
Google Scholar
Allaby RG, Brown TA. Network analysis provides insights into evolution of 5S rDNA arrays in Triticum and Aegilops. Genetics. 2001;157(3):1331–41.
CAS
PubMed
PubMed Central
Google Scholar
Baum BR, Edwards T, Johnson DA. Phylogenetic relationships among diploid Aegilops species inferred from 5S rRNA units. Mol Phylogenet Evol. 2009;53:34–44.
Article
CAS
PubMed
Google Scholar
Baum BR, Edwards T, Johnson DA. Co-dependence of repetitive sequence classes in genomes: the phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae). Genome. 2010;53:180–202.
Article
CAS
PubMed
Google Scholar
Badaeva ED, Friebe B, Gill BS. Genome differentiation in Aegilops. 2. Physical mapping of 5S and 18S-26S ribosomal RNA gene families in diploid species. Genome. 1996;39(6):1150–8.
Article
CAS
PubMed
Google Scholar
Badaeva ED, Friebe B, Gill BS. Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosome of diploid species. Genome. 1996;39(2):293–306.
Article
CAS
PubMed
Google Scholar
Raskina O, Belyayev A, Nevo E. Quantum speciation in Aegilops: molecular cytogenetic evidence from rDNA cluster variability in natural populations. Proc Natl Acad Sci U S A. 2004;101(41):14818–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baum BR, Edwards T, Mamuti M, Johnson DA. Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from the nuclear 5S rDNA sequences (Poaceae: Triticeae). Genome. 2012;55(3):177–93.
Article
CAS
PubMed
Google Scholar
Belyayev A, Raskina O. Chromosome evolution in marginal populations of Aegilops Speltoides: causes and consequences. Ann Bot. 2013;111(4):531–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shcherban AB, Sergeeva EM, Badaeva ЕD, Salina EA. Analysis of 5S rDNA changes in synthetic allopolyploids Triticum×Aegilops. Molecular Biology (Russ). 2008;42(4):604–11.
CAS
Google Scholar
Baum BR, Feldman M. Elimination of 5S DNA unit classes in newly formed allopolyploids of the genera Aegilops and Triticum. Genome. 2010;53(6):430–8.
Article
CAS
PubMed
Google Scholar
Staňková H, Hastie AR, Chan S, Vrána J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo M, Batley J, Edwards D, Doležel J, Šimková H. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnol J. 2016;14(7):1523–31.
Article
PubMed
PubMed Central
Google Scholar
Nesterov MA, Afonnikov DA, Sergeeva EM, Miroshnichenko LA, Bragina MK, Bragin AO, Vasiliev GV, Salina EA. Identification of microsatellite loci based on BAC sequencing data and their physical mapping into the soft wheat 5B chromosome. Russ J Genet: Appl Res. 2016;6(8):825–37.
Article
CAS
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local lignment search tool. J Mol Biol. 1990;215:403–10.
Article
CAS
PubMed
Google Scholar
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. Primer3 - new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C. Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J. 2010;8(2):196–210.
Article
CAS
PubMed
Google Scholar
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9.
Article
CAS
PubMed
Google Scholar
Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111–20.
Article
CAS
PubMed
Google Scholar
SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL. The paleontology of intergene retrotransposons of maize. Nat Genet. 1998;20:43–5.
Article
CAS
PubMed
Google Scholar
Ma J, Bennetzen JL. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 2004;101:12404–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113.
Article
PubMed
PubMed Central
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next generation sequencing data. Bioinformatics. 2012;28(23):3150–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acid Res. 1981;9(1):133–48.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salina EA, Lim YK, Badaeva ED, Shcherban AB, Adonina IG, Amosova AV, Samatadze TE, Vatolina TY, Zoshchuk SA, Leitch AR. Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids. Genome. 2006;49(8):1023–35.
Article
CAS
PubMed
Google Scholar
Bedbrook JR, Jones J, O’Dell M, Thompson RD, Flavell RB. A molecular description of telomeric heterochromatin in Secale species. Cell. 1980;19:545–60.
Article
CAS
PubMed
Google Scholar
Rayburn AL, Gill BS. Isolation of a D-genome specific repeated DNA sequence from Aegilops squarrosa. Plant Mol Biol Rep. 1986;4:102–9.
Article
CAS
Google Scholar
Smirnov AV, Entelis NS, Krasheninnikov IA, Martin R, Tarassov IA. Specific features of 5S rRNA structure – its interactions with macromolecules and possible functions. Biochemistry (Mosc). 2008;73:1418–37.
Article
CAS
Google Scholar
Badaeva ED, Ruban AS, Zoshchuk SA, Surzhikov SA, Knupffer H, Kilian B. Molecular cytogenetic characterization of Triticum timopheevii chromosomes provides new insight on genome evolution of T. zhukovskyi. Plant Syst Evol. 2016;302:943–56.
Article
Google Scholar
Gerlach WL, Dyer TA. Sequence organization of the repeated units in the nucleus of wheat which contains 5S-rRNA genes. Nucleic Acid Res. 1980;8:4851–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nieto Feliner G, Rossello JA. Concerted evolution of multigene families and homeologous recombination. In Plant Genome Diversity, Wien, Springer. 2012;1:171–94.
Article
Google Scholar
Dover GA. Molecular drive: a cohesive mode of species evolution. Nature. 1982;299:111–7.
Article
CAS
PubMed
Google Scholar
Eickbush TH, Eickbush DG. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics. 2007;175:477–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dubcovsky J, Dvorak J. Ribosomal RNA multigene loci–nomads of the Triticeae genomes. Genetics. 1995;140:1367–77.
CAS
PubMed
PubMed Central
Google Scholar
Shishido R, Sano Y, Fukui K. Ribosomal DNAs: an exception to the conservation of gene order in rice genomes. Mol Gen Genet. 2000;263:586–91.
Article
CAS
PubMed
Google Scholar
Davison J, Tyagi A, Comai L. Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis Thaliana. BMC Plant Biol. 2007;7:44.
Article
PubMed
PubMed Central
Google Scholar
Britton-Davidian J, Cazaux B, Catalan J. Chromosomal dynamics of nucleolar organizer regions (NORs) in the house mouse: micro-evolutionary insights. Heredity. 2012;108:68–74.
Article
CAS
PubMed
Google Scholar
Wicker T, Guyot R, Yahiaoui N, Keller B. CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Physiol. 2003;132:52–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kalendar R, Tanskanen J, Chang W, Antonius K, Sela H, Peleg O, Schulman AH. Cassandra retrotransposons carry independently transcribed 5S rRNA. Proc Natl Acad Sci U S A. 2008;105:5833–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cioffi MB, Martins C, Bertollo LA. Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus Erythrinus. Implications for genome change and karyoevolution in fish. BMC Evol Biol. 2010;10:271.
Article
PubMed
PubMed Central
Google Scholar
Lim KY, Matyasek R, Lichtenstein CP, Leitch AR. Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma. 2000;109:245–58.
Article
CAS
PubMed
Google Scholar
Kovarik A, Dadejova M, Lim K-Y, 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;101:815–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pontes O, Neves N, Silva M, Lewis MS, Madlung A, Comai L, Viegas W, Pikaard CS. Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis Suecica genome. Proc Natl Acad Sci U S A. 2004;101:18240–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Paule MR, White RJ. Survey and summary: transcription by RNA polymerases I and III. Nucleic Acids Res. 2000;28:1283–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kapitonov VV, Jurka J. A novel class of SINE elements derived from 5S rRNA. Mol Biol Evol. 2003;20:694–702.
Article
CAS
PubMed
Google Scholar
Hourcade D, Dressler D, Wolfson J. The amplification of ribosomal RNA genes involves a rolling circle intermediate. Proc Natl Acad Sci U S A. 1973;70:2926–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cohen S, Agmon N, Sobol O, Segal D. Extrachromosomal circles of satellite repeats and 5S ribosomal DNA in human cells. Mob DNA. 2010;1:11.
Article
PubMed
PubMed Central
Google Scholar
Navratilova A, Koblizkova A, Macas J. Survey of extrachromosomal circular DNA derived from plant satellite repeats. BMC Plant Biol. 2008;8:90.
Article
PubMed
PubMed Central
Google Scholar
Dvorak J, Di Terlizzi P, Zhang HB, Resta P. The evolution of polyploid wheats: identification of the a genome donor species. Genome. 1993;36:21–31.
Article
CAS
PubMed
Google Scholar
Dvorak J, Zhang HB. Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc Natl Acad Sci U S A. 1990;87:9640–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kovarik A, Matyasek R, Lim KY, Skalicka K, Koukalova B, Knapp S, Chase M, Leitch AR. Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids. Biol J Linn Soc. 2004;82:615–25.
Article
Google Scholar
Shcherban AB, Badaeva ED, Amosova AV, Adonina IG, Salina EA. Genetic and epigenetic changes of rDNA in a synthetic allotetraploid Aegilops sharonensis x Ae. Umbellulata. Genome. 2008;51(4):261–71.
Article
CAS
PubMed
Google Scholar
Guo X, Han F. Asymmetric epigenetic modification and elimination of rDNA sequences by polyploidization in wheat. Plant Cell. 2014;26:4311–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grummt I, Pikaard CS. Epigenetic silencing of RNA polymerase I transcription. Nat Rev Mol Cell Biol. 2003;4:641–9.
Article
CAS
PubMed
Google Scholar
Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007;8:973–82.
Article
CAS
PubMed
Google Scholar
Wicke S, Costa A, Munoz J, Quandt D. Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants. Mol Phylogenet Evol. 2011;61:321–32.
Article
CAS
PubMed
Google Scholar