Hello Cristina,

I have recently compared the sequences of rRNA genes among different operons of AAB, and I found out that in some genomes there are mistakes, probably the automatic annotation sometimes makes mistakes. You can try to find out if this is a case also in your genomes for example by Blast analysis of one copy rRNA gene to the entire genome.

Best regards,

Janja

Thanks to everyone for your answers.

You're talking about minor differences in the sequence of rRNAs subuntis of different operons, but in my case the differences are huge, as high as 50% and no clearly defined fragment is conserved. Please, see the alignment attached. 

On the other hand, I also agree ITS may or may ynot contain tRNAs…, but the annotation of 2 tRNA inside the 23S rRNA do not make sense for me… neither do the codification of a protein inside a 16S rRNA sequence. What do you think about this?

Dear Dr. Trcek, thank you very much for your answer, that's what I did effectively, and that's why I discovered what I think are genomic inconsistencies, probably due to mistakes in the automatic annotation. I did once, a while ago, the comparison of the genome of A. pasteurinaus, the first 8 genomes publicly available, and found some differences in the annotation of the rRNA operons. I'm going to verify this again. The use of a good reference for RNA-Seq data analysis is of paramount importance and I'm afraid we have been using up to now a wrong one. 

Best regards

Dear Cristina,

Just a comment. As  Dr. Trcek said,  usually people do genomic annotation with automatic annotation pipelines and do not apply a manual curation step (the most time consuming) that usually correct the errors you exposed. My suggestion is that you should take some time looking at the genome and fix this kind of problems before map your RNA. Also take in mind that you can accumulate errors during genome assembly (i.e. 16S rRNA is usually so difficult to assemble correctly with NGS).

Best,

Diego