Microarray-based survey of repetitive genomic sequences in Vicia spp.

Marcela Nouzová, Pavel Neumann, Alice Navrátilová, David W. Galbraith, Jiří Macas

Research output: Contribution to journalArticle

32 Scopus citations

Abstract

A modified DNA microarray-based technique was devised for preliminary screening of short fragment genomic DNA libraries from three Vicia species (V. melanops, V. narbonensis, and V. sativa) to isolate representative highly abundant DNA sequences that show different distribution patterns among related legume species. The microarrays were sequentially hybridized with labeled genomic DNAs of thirteen Vicia and seven other Fabaceae species and scored for hybridization signals of individual clones. The clones were then assigned to one of the following groups characterized by hybridization to: (1) all tested species, (2)most of the Vicia and Pisum species, (3) only a few Vicia species, and (4) preferentially a single Vicia species. Several clones from each group, 65 in total, were sequenced. All Group I clones were identified as rDNA genes or fragments of chloroplast genome, whereas the majority of Group II clones showed significant homologies to retroelement sequences. Clones in Groups III and IV contained novel dispersed repeats with copy numbers 102-106/1C and two genus-specific tandem repeats. One of these belongs to the VicTR-B repeat family, and the other clone (S12) Contains an amplified portion of the rDNA intergenic spacer. In situ hybridization using V. sativa metaphase chromosomes revealed the presence of the S12 sequences not only within rDNA genes, but also at several additional loci. The newly identified repeats, as well as the retroelement-like sequences, were characterized with respect to their abundance within individual genomes. Correlations between the repeat distributions and the current taxonomic classification of these species are discussed.

Original languageEnglish (US)
Pages (from-to)229-244
Number of pages16
JournalPlant Molecular Biology
Volume45
Issue number2
DOIs
StatePublished - Apr 2 2001

Keywords

  • DNA microarrays
  • Plant genome organization
  • Repetitive DNA
  • Retroelements
  • Satellite DNA
  • Vicia

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science

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