I have checked many research papers to find the %G+C content of whole bacterial genomes. Can the %G+C content of the whole bacterial genome be estimated by the %G+C content of the 16S rDNA sequence? In other ways, can we estimate the %G+C content of the whole bacterial genome from 16S rDNA sequence and can we say that %G+C content of the whole bacterial genome is equal to %G+C content of the 16S rDNA sequence?
That is a definite no. For example, Streptomyces species have G+C contents of up to 73% while their RRNs have a G+C of ~55%. And the conventional methods often give results that diverge strongly from the real content. For a rough estimation, I would recommend random sequencing of ~10kbp.
To estimate the GC content of any DNA or RNA fragments you can use
DNA/RNA GC Content Calculator (http://www.endmemo.com/bio/gc.php).
But I think it can give you only limited size, however, we can use similar algorithms for extra large fragments .
Concerning the HPLC approach: For some reason that often tends to give incorrect values. We have sequenced quite a lot of high G+C bacteria and the real content was usually 2-5% higher than the one published for HPLC. In one case it was almost 10% higher. As the HPLC values came from different groups, I figure that there is some flaw with the methodology in this case. But I am at a loss why this happens.
Concerning the estimation approach by random sequencing: isolate gDNA, fragment into pieces of 500-2000 bp, clone into a vector of your choice and sequence 10-20. Then just count The good quality bases of the results. For large genomes I recommend going for ~20kb.
The "best" way is to do a WGS approach. But that is still not cheap...
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology