Dear all,
As part of my study, I downloaded candidate genes for a particular gene family of Lotus japonicus and Medicago truncatula. Unfortunately, I encountered four pairs from Mt and six pairs from Lj showed 100% identity in amino acid level. Then I verified their genomic sequences, CDS and 2 Kb upstream/downstream regions. Some pairs showed 100% identity in every category while some pairs showed SNPs either in intron or in up/down stream regions. Interestingly, Some 100% identical pairs are tandem duplicates while some are segmental duplicates.
Is it possible 100% identical duplicated genes could exist in Mt and Lj genomes? Should I think about sequencing error?
PS: I just knew that some ribosomal paralogs shared 100% amino acid identity in Arabidopsis and other species.,
Dear Panneerselvam,
Unfortunately, you have not provided information sufficient for exact answer. Personally, I have met several errors in identification of organisms assigned to the GeneBank sequence. Especially, sequences of symbiotic/parasitic organisms were identified as DNA fragments of corresponding host organism.
With Regards
Alex
Dear,
Don't faith in data generated by tools , there are chances of similarity but not 100% that is totally wrong. I personally request you donot faith in tools and sequence generated by some prominent sites too. such accidents can happen . simply you search QTL map of single crops and read chromosomes from at least five paper from any journal and compare you will realized whats going on the data generated by software tools and person.
sorry dear"
I suggest to check your sequences align them carefully at nucleotide and amino acid level to identify the codons where could have point mutations, and other bioinformatic tools; and also try to use reference genomes to ensure a more accurate and better supported analysis of your data.
Albeit, at amino acid level 100% could be possible, may generate some questioning. And talking about legume species, you have to take into account that several species had been experienced genome duplication (tetraploidism) and back again into a diploid genome, that leaves too many duplicated sequences among species by the sharing of a common ancestor; and even this kind of phenomena has been characterised in Arabidopsis. So, your result it might be possible.
Regards
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