How can Investigate if a Viral genome is circular or linear? And if it is single or double stranded?

Question

[GiV17]

Hi, I have assembled a new virus genome. So I have contigs and scaffolds fasta file. My question is:

1. How can I understand if this new viral genome is circular or linear, starting by contigs or scaffolds file?
2. How can I understand if it's single or double stranded?

Are there any tools, software or scripts that do this?

Please, Help me. Thanks Giovanna

[WouterDeCoster]

How can I understand if it's single or double stranded?

The easiest solution will be a wet-lab method.

[GiV17]

Thanks, but can you suggest me how?

[WouterDeCoster]

Spectrophotometry, like nanodrop or qubit, should be able to distinguish ssDNA from dsDNA.

[Joe]

Off the top of my head, a simple way would be to try and restriction digest your DNA with double-strand specific restriction enzymes. If they work, its probably dsDNA, if not, probably ssDNA.

If you also have to consider RNA viruses things get more complicated, but I'm guessing if that was the case you wouldn't have NGS data for it already.

Answer 1

[5heikki]

Do you have paired-end reads? Yes? See how the map. You should have pairs with R1 mapping towards the 5'-end of the assembly with R2 mapping towards the 3'-end (or vice versa). The process is more complicated if you have many contigs (which seems pretty odd for a viral genome assembly). Another tell tale is if the 5'-end of the contig and the 3'-end of the contig (again assuming just one contig assembly) overlap with e.g. self-vs-self blast query..

[GiV17]

Hi, yes I have paired reads and I have many contigs. So how can I do?

[5heikki]

First map the reads to your assembly. Then filter away all pairs that map near to each other. See what remains. Be sure to allow the reads to map to multiple loci. It's not so easy to answer because you have told us very little about your data. Where did the nucleic acids come from and how were they isolated, sequenced and assembled? Etc. Stuff like this alone could maybe answer questions about ssDNA vs dsDNA..

[GiV17]

I had paired fastq file that were mapped with Genieous and I obtained the contigs fasta file. Then I performed SOPRA scaffolding and the statistics of its. Now I would like to know if my genome is single or double stranded and if it is circular or linear. Now I'm testing Circlator, but it is still running. Do you have any other ideas? Thanks all.

[Israel]

Hi, I have several questions, why did you circularize the contig? and what is the use of detecting circular fastq files?? I'm working with virome but in patients with metabolic syndrome and I am still learning the methodology to analyze my data

Answer 2

[Joe]

I don't think you can easily, if at all, figure out the strandedness of the virus.

As 5hekki points out, in order to decide if it's circular, you can just look to see if the sequences are circularly permuted at each end.

The following tool might be useful:

https://github.com/sanger-pathogens/circlator