Intraspecific Variability and Distribution Difference within the Ribosomal Introns of the Discrete Plasmodiophora brassicae Group in Japan: A Case Study for Complex Dynamics of Intron Evolution

Abstract

Analysis of the ribosomal introns of Plasmodiophora brassicae populations infecting the cruciferous weed Cardamine occulta revealed the complex dynamics of size, intraspecific variability, and distribution. The results showed that P. brassicae populations from the weed have lost multiple introns in the small and large subunits of the ribosomal RNA genes. Moreover, the retained introns, despite a largely mutual share of conserved parts with the cosmopolitan strains, contained numerous novel structures. These structural differences comprise a high level of polymorphisms, such as transversion point mutations occurring at sites involving the intronic splicing sites or insertions/deletions at the binding sites. Two geographical P. brassicae populations from C. occulta carried a lengthy intron-encoded ORF and putative mobile elements established in the large subunit. A few P. brassicae populations from the Brassica crops also harbored polymorphic introns that shared common mutated motifs with the weed-affecting group. The diversity of ribosomal introns observed from those investigated populations demonstrated the genetic distinction of the P. brassicae populations from C. occulta. The genetic variations might play a key role in the adaptability of the weed-infecting populations and are more likely related to the process of pathogenesis for the cosmopolitan P. brassicae infecting the Brassica crops.