Differences in DRR machinery among plants
Despite of strong conservation of DRR proteins, we have observed intriguing difference in DRR genes in plant genomes also. This difference ranges from difference in number of homlogs to the absence or presence of a particular protein (Additional file 1). For example Arabidopsis have been found to contain two paralogous copies of xeroderma pigmentosum complementation group B (XPB), a component of the transcription factor IIH (TFIIH), gene. Analysis of the presence of XPB gene in different plant genomes including rice, Medicago trunculata, Carica papaya, Vitis venifera, Zea mays, Glycine max, sorghum and populus have indicated that beside Glycine max none of the analyzed plant genome has two paralogs for XPB genes. Both genes (Joint Genome Institute accession number-Glyma08g01970 and Glyma05g37610) of Glycine max were found to be originated from intergenomic duplication from Arabidopsis. These results indicated towards genus specific expansion of XPB and worth further investigation. FEN1, a nuclease, show an interesting pattern of evolution. All monocotyledonous genomes we analyzed, rice, Zea mays, sorghum and Brachypodium, were found to contain two copies of FEN1 and these copies were not the products of intragenomic duplication. On the other hand, all the dicotyledonous genomes that we have studied, Arbidopsis, Medicago trunculata, Vitis venifera, Glycine max and populous, have single copy of FEN1 except Glycine max. These copies of FEN1 in Glycine max were the product of intragenomic duplication and, unlike monocotyledonous FEN1 genes, acquire same node on phylogenetic tree (our unpublished data). Thus, FEN1 shows lineage specific evolution. Significant difference has also been observed in the duplication level in DRR genes of Arabidopsis and rice. Taken together, these results possibly reflecting some differences in the mechanisms and pathways by which damaged DNA are repaired by Arabidopsis and rice genomes.