I want to make a phylo tree using the 16S rRNA gene of the complete Aeromonas hydrophila genomes/strains available from GenBank. But each genome has several 16S rRNA genes (as many as 10) and they may have different sequences.
Do I just select one and omit the rest? Do them one by one (but takes a lot of time as there are many existing genomes)?
Hi,
Ribosomal RNA genes or spacer regions (e.g., ITS) are generally conserved with an organism. Even if there are multiple genes (100-1000 copies) the regions are conserved due to the mechanisms operating in the background. Hence, in general a single sequence is fine for phylogenetic analysis. However, if evidence shows presence of paralogs, do not reply on a single sequence. Analyze the heterogeneity among the paralogs and use the a representative sequence carefully. You may also use many of them, in the same analysis, however try to avoid if some of them appear to be pseudogenic in nature. If the paralogs have very less divergence, they will cluster together, which may not change there relationships with other species. Phylogenetic inferences may become problematic if the clustering of a species change when you use different paralogs. There are several studies where problems associated with the use of rRNA gene paralogs have been discussed. Go through some such publications.
Kenneth Joseph Chan Bureros Just try to cluster all sequences from the same organism at 100% identity using cd-hit. If all sequences are identical or