Abstract
EcoRI restriction of theB. nigra rDNA recombinants, isolated from a lambda genomic library, showed that the 3.9-kb fragment corresponded to the Intergenic Spacer (IGS), which was sequenced and found to be 3,928 by in size. Sequence and dot-matrix analyses showed that the organization of theB. nigra rDNA IGS was typical of most rDNA spacers, consisting of a central repetitive region and flanking unique sequences on either side. The repetitive region was composed of two repeat families—RF ‘A’ and RF ‘B.’ TheB. nigra RF ‘A’ consisted of a tandem array of three full-length copies of a 106-bp sequence element. RF ‘B’ was composed of 66 tandemly repeated elements. Each ‘B’ element was only 21-bp in size and this is the smallest repeat unit identified in plant rDNA to date. The putative transcription initiation site (TIS) was identified as nucleotide position 3,110. Based on the sequence analysis it was suggested that the present organization of the repeat families was generated by successive cycles of deletions and amplifications and was being maintained by homogenization processes such as gene conversion and crossing-over.
A detailed comparison of the rDNA IGS sequences of the three diploidBrassica species—namely,B. nigra, B. campestris, andB. oleracea—was carried out. First, comparisons revealed thatB. campestris andB. oleracea were close to each other as the repeat families in both showed high sequence homology between each other. Second, the repeat elements in both the species were organized in an interspersed manner. Third, a 52-bp sequence, present just downstream of the repeats inB. campestris, was found to be identical to theB. oleracea repeats, thereby suggesting a common progenitor. On the other hand, inB. nigra no interspersion pattern of organization of repeats was observed. Further, theB. nigra RF ‘A’ was identified as distinct from the repeat families ofB. campestris andB. oleracea. Based on this analysis, it was suggested that during speciationB. campestris andB. oleracea evolved in one lineage whereasB. nigra diverged into a separate lineage. The comparative analysis of the IGS helped in identifying not only conserved ancestral sequence motifs of possible functional significance such as promoters and enhancers, but also sequences which showed variation between the three diploid species and were therefore identified as species-specific sequences.
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Correspondence to: M. Lakshmikumaran
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Bhatia, S., Negi, M.S. & Lakshmikumaran, M. Structural analysis of the rDNA intergenic spacer ofBrassica nigra: Evolutionary divergence of the spacers of the three diploidBrassica species. J Mol Evol 43, 460–468 (1996). https://doi.org/10.1007/BF02337518
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DOI: https://doi.org/10.1007/BF02337518