Application of the deRIP process to the Molly transposon repeat family of Stagonospora nodorum SN15. Molly is one of three S. nodorum repeats with known functionally transposable sequence available [NCBI AJ488502.1]. (A) Genomic matches to the Molly repeat family were aligned and compared for RIP-like polymorphism against a model sequence (in this case the majority consensus). RIP mutation of the form CpN ←→ TpN was color-coded as indicated in the legend. (B) The deRIP process was applied to a 51 bp sub-region of the alignment. A 'majority' consensus of the alignment represented the most abundant nucleotide at each alignment position. The deRIP consensus was derived from the majority consensus, however where di-nucleotides were detected exhibiting RIP-like polymorphism (Table 1) they were reverted back to their pre-RIP state. Changes in sequence between majority and deRIP consensus sequences was compared to the sequence of the active transposon. (C) Phylogram showing relationships between all genomic regions, majority consensus, deRIP consensus and active copy of the Molly repeat family. The deRIP consensus resembled the functional transposon more closely than the majority consensus, highest G:C content sequence and the majority of matching genomic regions.
Hane and Oliver BMC Genomics 2010 11:655 doi:10.1186/1471-2164-11-655