FokI DNA repeats in the genome of Vicia faba: species specificity, structure, redundancy modulation, and nuclear organization

Abstract

Tandemly repeated DNA sequences about 60 bp in length, which may be isolated by digestion with FokI restriction endonuclease, were studied by means of molecular and cytological hybridization in Vicia faba and other Vicia species. The results obtained can be summarized as follows: (i) FokI repeats are almost species specific to V. faba, since they hybridize to a minimum extent to genomic DNA of only two out of five related species; (ii) these tandemly repeated elements display variability in structure even within one and the same array, where different repeats may share not more than 71% homology; (iii) their redundancy in the genome of V. faba is remarkably high and varies largely between land races (copy numbers per haploid, 1C, genome range from 21.51 x 10(6) to 5.39 x 10(6)); (iv) FokI repeats are clustered in differing amounts in each subtelocentric pair of the chromosome complement and are missing or present in a nondetectable amount in the submetacentric pair; (vi) chromosome regions that bear these repeats associate closely to varying degrees in interphase nuclei. These results are discussed in relation to possible functional roles that tandemly repeated DNA sequences such as the FokI elements might play.

Cytology of Vicia Species. 5. Nuclear Chromatin Structure, Karyomorphological Analysis and DNA Content in Newly Discovered Relatives of Vicia faba L.: Vicia kalakhensis Khattab, Maxted et Bisby and Vicia eristalioides Maxted.

“…The results of molecular analysis (Raina and Oghihara 1995) do not support diversity in the Narbonensis complex even if the authors have not analysed V. eristalioides. On the contrary the results obtained by studying the FokI elements in the genomes of V. faba and other Vicia species (Maggini et al 1995), using biochemical approaches, support diversity in the Narbonensis complex. DNA sequences related to the FokI elements are not detectable even in species (V. galilea, V. hyaenisciamus, V. johannis) that belongs to the Narbonensis complex and are represented to a minimum extent in V. narbonensis.…”

“…In previous papers biochemical and cytophotometric data on Vicia species belonging to the Faba section have been reported (Cremonini et al 1992, Frediani et al 1992, Maggini et al 1995. The karyological relationships among the species of this section had been analysed at both cytological and banding levels (Schafer 1973, Perrino andPignone 1981).…”

Genome size variation in Vicia faba

“…The coverslips were removed by the solid CO2 method and the preparations were Feulgen-stained after different hydrolysis durations in N HC1 at 60°C: 8 mm for those made with material fixed in ethanol-acetic acid and 20 mm for those made with formalin-fixed material. After staining, the slides were subjected to three 10 mm washes in SO2 water prior to dehydration and mounting in DPX (BDH Tandem arrays of FokI repeats about 300 bp in length were isolated from V. faba genomic DNA by digestion with Sau3AI and RsaI restriction endonucleases, and subcloned in pBS-vectors, as described by Maggini et al (1994).…”

Repetitive DNA sequences as probes for phylogenetic analysis in Vicia genus

“…In previous papers, we reported cytological, karyological and biochemical data in order to elucidate the relationships inside Vicia subgenus (Cremonini et al 1998 a, b;Frediani et al 1992Frediani et al , 1999Maggini et al 1991Maggini et al , 1995Venora et al 2000).…”

“…In this paper we report new experimental evidence based on the use of four different molecular markers belonging to the heterogeneous class of repeated DNA sequences; three of these molecular markers have been previously used to study the structure of the genome of V. faba. The first marker we used was FokI, a family of tandemly repeated DNA sequences about 60 bp in length, which represents a considerable portion of the genome of V. faba (Kato et al 1984;Maggini et al 1995); the second, named pVf7 repeats, represents another family of repetitive DNA related to sequences founded in Intergenic Spacer (IGS) of ribosomal DNA and spread in centromeric and telomeric regions of V. faba (Kato et al 1985;Maggini et al 1991); VfB represents a family of repeated DNA sequences of about 1200 bp in length which are dispersed in the genome of broad bean and absent or rare only at the hetero-chromatic chromosomal regions (Frediani et al 1999). The last marker, termed VfM, is a minisatellite-like sequence isolated in a V. faba library.…”