Forward and Reverse strand on gene annotation

Question

[DanielC]

Dear Friends,

I annotated an assembled phage using DNAMAster. The ORF map is below. Could you please help me understand why we see more revere strands then forward strands? Shouldn't hey have same numbers? green ones are forward and red ones are reverse.

Thanks, DK

Answer 1

[Joe]

More ORFs on one strand than the other you mean?

No, there's no requirement that there be approximately equal ORF distribution on each strand. Often it would roughly average out to be the case, but its not wholly uncommon to have long stretches where the majority of the ORFs are on one strand, then it may switch to the other strand for a while. The oscillation then averages out over the whole genome length roughly in many cases.

[DanielC]

Yes, as shown in the figure. Thanks for your answer; however, could you please tell me what you mean by "switching of ORFs"? Do ORFs switch between DNA strands?

[Joe]

Depends how you define it. An ORF could appear on either strand, if the DNA reinserted the other way around. This does happen in recombination. The ORF itself as a 'concept' cannot move though, because it's tied to the sequence, the actual physical DNA would have to switch orientation.

What I meant by what I said before, is that its not uncommon to have a cluster of (say) 20 genes on one strand, that are perhaps all part of the same operon, and therefore group together syntenically. Once that operon is 'finished' the next gene cluster may, by chance, or for some evolutionary reason, be on the other strand.

The only thing that is less common in most organisms (phage/viruses and other organisms with extremely streamlined genomes are exceptions), is that its very rare to have genes directly opposite one another on each strand. This is rarer because the sequence of the first gene places constraints on what possible sequences can be present on its complementary strand. Evolution is clever though, and there are cases, as I say, where 2 ORFs can be directly opposite one another, if the 'space of possible sequences' allows.

PS. your figure hasn't displayed properly, you're best off copying in the direct HTML.