Structural analysis of two length variants of the rDNA intergenic spacer from Eruca sativa

Abstract

Restriction enzyme analysis of the rRNA genes of Eruca sativa indicated the presence of many length variants within a single plant and also between different cultivars which is unusual for most crucifers studied so far. Two length variants of the rDNA intergenic spacer (IGS) from a single individual E. sativa (cv. Itsa) plant were cloned and characterized. The complete nucleotide sequences of both the variants (3 kb and 4 kb) were determined. The intergenic spacer contains three families of tandemly repeated DNA sequences denoted as A, B and C. However, the long (4 kb) variant shows the presence of an additional repeat, denoted as D, which is a duplication of a 224 bp sequence just upstream of the putative transcription initiation site. Repeat units belonging to the three different families (A, B and C) were in the size range of 22 to 30 bp. Such short repeat elements are present in the IGS of most of the crucifers analysed so far. Sequence analysis of the variants (3 kb and 4 kb) revealed that the length heterogeneity of the spacer is located at three different regions and is due to the varying copy numbers of repeat units belonging to families A and B. Length variation of the spacer is also due to the presence of a large duplication (D repeats) in the 4 kb variant which is absent in the 3 kb variant. The putative transcription initiation site was identified by comparisons with the rDNA sequences from other plant species.

Characterization of the nuclear ribosomal DNA unit in Oxalis tuberosa Oxalidacea and related species

“…villosula and O. tuberosa) shows that they share the same general organization found in many plants species, particularly the location of BamHI, EcoRI and EcoRV restriction endonuclease sites found here are essentially as those found in other species (see Doyle and Beachy, 1985;Rogers and Bendich, 1987;Zimmer, 1988;Crisci et al 1990;Lakshmikumaran et al 1994;Warpeha et al 1998;Bhagwat et al 2001;Pillay and Kenny, 2006, for some examples).…”

“…enzyme digestion coupled whit Southern hybridization (Appels et al 1980;Appels and Dvorack, 1982;Grellet et al 1989;Sano and Sano, 1990;Clegg, 1990;Maggini et al 1992;Lakshmikumaran et al 1994;Cluster et al 1996;Jeandroz et al 1996;Gupta et al 2002 and reference there are in; Skalická et al 2003;Lim et al 2004;Kovarik et al 2005).…”

Structural analysis of the rDNA intergenic spacer ofBrassica nigra: Evolutionary divergence of the spacers of the three diploidBrassica species

“…The rDNA IGS is among the best-studied spacer sequences among plants and has been characterized from Eruca sativa (Lakshmikumaran and Negi 1994), potato (Borisjuk and Hemleben 1993), rice (Cord- esse et al 1993), Brassica oleracea , Pharbitis nil (Katayama et al 1992), Sinapis alba (Rathgeber and Capesius 1990), cucumber (Zentgraf et al 1990), pea (Piller et al 1990), Arabidopsis (Gruendler et al 1989(Gruendler et al , 1991, tomato (Schmidt-Puchta et al 1989), wheat (Barker et al 1988), radish (Delcasso- Tremousaygue et al 1988), carrot (Taira et al 1988), mungbean (Gerstner et al 1988, maize (Toloczyki and Feix 1986;McMullen et al 1986), and rye (Appels et al 1986). The molecular basis for length heterogeneity may be attributed to variations in the copy number of the repeat elements present within the IGS as observed in E. sativa (Lakshmikumaran and Negi 1994), Arabidopsis (Gruendler et al 1991), pea (Piller et al 1990), carrot (Taira et al 1988), maize (McMullen et al 1986), Viciafaba (Yakura et al 1984), and wheat (Gerlach and Bedbrook 1979). The IGS of almost all plant species studied so far exhibits length and sequence heterogeneity.…”

Structure and Comparative Analysis of the rDNA Intergenic Spacer of Brassica rapa. Implications for the Function and Evolution of the Cruciferae Spacer

“…[20]) as a model. The availability of spacer sequences representative of five genera and two tribes of the same plant family, including those of B. rapa, R. sarivus [3], Sinapis alba [23], Arabidopsis thaliana [24], B. oleracea [20,251 and Eruca sativa [26], is exploited for comparative analysis and to obtain information on the structure and evolution of the Cruciferue IGS. F., Xia, J. X. and Bertrand, H., unpublished results).…”