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Phylogenetic analyses within three sections of the genus Vicia

Abstract

The averaged genomic similarities based on multilocus randomly amplified polymorphic DNA (RAPD) were calculated for eight species representing three sections of the genus Vicia: faba, bithynica and narbonensis. The frequency of appearance of the sequences corresponding to 25 decamers selected at random from genomes of different Fabace species was checked, and a high correlation with the frequency observed for Vicia allowed us to assume their similar weight in typing Vicia species. The RAPD-based similarity coefficients compared with those related to whole genome hybridization with barley rDNA and those based on restriction fragment length polymorphism (RFLP) revealed similar interspecies relationships. The averaged RAPD-based similarity coefficient (Pearson’s) was 0.68 for all the species, and was sectionspecific: 0.43 (bithynica), 0.50 (faba) and 0.73 (narbonensis). The averaged similarity coefficient for V. serratifolia (0.63) placed it apart from the rest (0.75) of its section. The results correspond to the interspecies relationships built upon non-genetic data. The averaged similarity coefficient for particular RAPD was related to the presence and type of tandemly repeated motif in a primer: 0.7–0.8 for heterodimers (GC, AG, CA, GT, CT), 0.5–0.6 for homodimers (CC, GG) and 0.6 for no repeat, indicating the sensitivity of diversity range to the type of target sequences.

Abbreviations

AFLP:

amplified fragment length polymorphism

BLAST:

basic local alignement search tool

EDTA:

ethylene diamine tetraacetic acid

HTGS:

high throughput genomic sequences

ICARDA:

International Center for Agricultural Research in the Dry Areas

ITS:

internal transcribed spacers

Mb:

mega base

Nr:

‘non redundant’

QTL:

quantitative trait loci

RAPD:

randomly amplified polymorphic DNA

RFLP:

restriction fragment length polymorphism

UPGMA:

unweighted pairs group method using mathematical avarages

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Sakowicz, T., Cieślikowski, T. Phylogenetic analyses within three sections of the genus Vicia . Cell Mol Biol Lett 11, 594–615 (2006). https://doi.org/10.2478/s11658-006-0047-x

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Key words

  • Vicia
  • Average similarity
  • Multilocus diversity
  • RAPD