The distribution of the Y1 family of rDNA repeats and their susceptibility to RIP mutation. (A) A multiple alignment of Y1 rDNA repeats found in the genome of S. nodorum strain SN15. Each repeat was compared for mutation with the alignment majority consensus (black = match, grey = mismatch, white = gap). The mutation of CpN di-nucleotides is color-coded according to the legend (left). In S. nodorum RIP is characterised by the mutation of CpA di-nucleotides (red). Y1 rDNA repeats are grouped according to their genomic location and length. Full length rDNA repeats scattered randomly throughout the genome are prone to RIP whereas short, incomplete copies (defined as <1 kb but generally <300 bp) are not affected. rDNA repeats located in a tandem array at the 3' end of scaffold 5 [NCBI: CH445329] are protected from RIP, excepting a single repeat. (B) The S. nodorum tandem rDNA array, also known as the nucleolus organiser region (NOR), and flanking regions. Region 1 contains gene encoding regions, region 2 contains non-rDNA repeats and regions 3 and 4 comprise the tandem rDNA array. RIP mutates repetitive DNA, hence genes in region 1 are not RIP-mutated but repeats in region 2 are RIP-mutated (indicated in red). The tandem rDNA array repeats are protected from RIP (region 4), except for a single repeat at the array terminus (region 3).
Hane and Oliver BMC Genomics 2010 11:655 doi:10.1186/1471-2164-11-655