PMC:3091640 / 6025-9238
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091640","sourcedb":"PMC","sourceid":"3091640","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091640","text":"Identification of DRR genes in rice and Arabidopsis\nIn order to study the conservation and evolution of DRR pathways in rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genomes, we examined the conservation of 229 and 223 gene models in Arabidopsis and rice respectively. Detail about every gene and number of paralogs present in Arabidopsis and rice genomes are tabulated in additional file 1 while the locus IDs and relevant plant literature (if available) is listed in additional file 2. The genomes of Arabidopsis and rice were searched for the presence of genes known to act in the metabolism of DNA lesions, mostly in human, Saccharomyces cerevisiae and E. coli. When a gene was not found, it indicates either that the gene was absent in the considered organism or that the sequence was too varied to be recognized using our criteria. Later on, genes of rice and Arabidopsis were also queried against each genome to check the consistency of the genes. Sequences were also manually checked for the presence of any wrong annotations. Few probable wrong annotations were found. For example, BLAST analysis revealed three loci, LOC_Os02g54280, LOC_Os02g54170 and LOC_Os02g54290, with significant hits for AtBRU1 in rice, a gene acts as a link between responses to DNA damage and epigenetic gene silencing in Arabidopsis. We discarded LOC_Os02g54290 because it did not contain the BRU1 specific domain. LOC_Os02g54170 was annotated as BRUSHY 1 while LOC_Os02g54280 was annotated as retrotransposon protein. CDD analysis has shown that LOC_Os02g54280 contain the BRU1 specific conserved domains, tetratricopeptide repeats (TPRs) and leucine-rich repeats (LRRs), with few additional domains like RnaseH (cd06222). LOC_Os02g54170 has shown to contain only LRRs and lack TPRs. Thus the possibility of wrong annotation for LOC_Os02g54280, as like LOC_Os02g54290, was high as it was highly similar to AtBRU1 (1.1e-140, 41.0% identity and 67.3% similar) and also contained all conserved domains. The identified DRR genes were found to be distributed on all the rice (3 to 17%) and Arabidopsis (12 to 30%) chromosomes. In rice, the highest number of DRR genes (17.48%) was predicted on chromosome 1, the longest chromosome in the rice genome. Similarly in Arabidopsis, the longest chromosomes 1 and 5 of Arabidopsis have been found to harbour the highest number of genes involved in DRR (29.91% and 23.21% respectively) (Additional file 3). Apparently, the distribution of DRR genes in terms of their involvement in different pathway seems uniform, however a strong bias towards clustering of genes involved in same pathway on different chromosome deserve special mention (Additional file 4).\nIn order to facilitate understanding of the major similarities and differences between two genomes, genes have been classified as: 1-Excision repair [base excision repair (BER), nucleotide excision repair (NER) and mismatch repair (MMR)]; 2- Double-Strand Break Repair [homologous recombination (HR) and non-homologous end joining (NHEJ)] and 3- Other DNA repair related genes. In the third category, we have assigned all those genes which are not catalogued in KEGG pathway database as the part of main DRR pathways.","divisions":[{"label":"title","span":{"begin":0,"end":51}},{"label":"p","span":{"begin":52,"end":2695}}],"tracks":[]}