title: Differential amplification of satellite PaB6 in chromosomally hypervariable Prospero autumnale complex (Hyacinthaceae).
abstract: OBJECTIVE
  Chromosomal evolution, including numerical and structural changes, is a major force in plant diversification and speciation. This study addresses genomic changes associated with the extensive chromosomal variation of the Mediterranean Prospero autumnale complex (Hyacinthaceae), which includes four diploid cytotypes each with a unique combination of chromosome number (x = 5, 6, 7), rDNA loci and genome size.
  
  
  METHODS
  A new satellite repeat PaB6 has previously been identified, and monomers were reconstructed from next-generation sequencing (NGS) data of P. autumnale cytotype B(6)B(6) (2n = 12). Monomers of all other Prospero cytotypes and species were sequenced to check for lineage-specific mutations. Copy number, restriction patterns and methylation levels of PaB6 were analysed using Southern blotting. PaB6 was localized on chromosomes using fluorescence in situ hybridization (FISH).
  
  
  RESULTS
  The monomer of PaB6 is 249 bp long, contains several intact and truncated vertebrate-type telomeric repeats and is highly methylated. PaB6 is exceptional because of its high copy number and unprecedented variation among diploid cytotypes, ranging from 10(4) to 10(6) copies per 1C. PaB6 is always located in pericentromeric regions of several to all chromosomes. Additionally, two lineages of cytotype B(7)B(7) (x = 7), possessing either a single or duplicated 5S rDNA locus, differ in PaB6 copy number; the ancestral condition of a single locus is associated with higher PaB6 copy numbers.
  
  
  CONCLUSIONS
  Although present in all Prospero species, PaB6 has undergone differential amplification only in chromosomally variable P. autumnale, particularly in cytotypes B(6)B(6) and B(5)B(5). These arose via independent chromosomal fusions from x = 7 to x = 6 and 5, respectively, accompanied by genome size increases. The copy numbers of satellite DNA PaB6 are among the highest in angiosperms, and changes of PaB6 are exceptionally dynamic in this group of closely related cytotypes of a single species. The evolution of the PaB6 copy numbers is discussed, and it is suggested that PaB6 represents a recent and highly dynamic system originating from a small pool of ancestral repeats.
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
authors.forename: Khatere
authors.initials: K
authors.lastname: Emadzade
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
authors.forename: Tae-Soo
authors.initials: TS
authors.lastname: Jang
authors.affiliation: Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Macas
authors.affiliation: Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
authors.forename: Ales
authors.initials: A
authors.lastname: Kovařík
authors.affiliation: Czech Academy of Sciences, Institute of Plant Molecular Biology, Ceske Budejovice, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Novák
authors.affiliation: Cambridge University Botanic Garden, Cambridge CB2 1JF, UK.
authors.forename: John
authors.initials: J
authors.lastname: Parker
authors.affiliation: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria hanna.schneeweiss@univie.ac.at.
authors.forename: Hanna
authors.initials: H
authors.lastname: Weiss-Schneeweiss
mesh_terms: D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics*; D056915:DNA Copy Number Variations; D018744:DNA, Plant / Q000235:genetics*; D004276:DNA, Satellite / Q000235:genetics*; D004171:Diploidy; D019143:Evolution, Molecular; D018745:Genome, Plant; D019668:Liliaceae / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D016615:Telomere / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D004276:DNA, Satellite
keywords: Hyacinthaceae; PaB6; Prospero autumnale; chromosomal evolution; copy number; differential amplification; fluorescence in situ hybridization (FISH); genome size; next-generation sequencing; pericentric satellite DNA