Can a dsRNA get sequenced on illumina with the 125bp pair end library meant for DNA sequencing?

Question

[jigarnt]

Hi All,

For some of you it might look as a completely stupid question but for me its important. Are there any chances of it happening? Can a dsRNA resist its way through RNAse degradation and get sequenced on illumina next gen platform, while using the 125bp pair end library for DNA?

I am possibly suspecting that it could be a mycovirus.

Eagerly awaiting for responses!!

[GenoMax]

You could also have contamination. One possible way to confirm. Design some PCR primers, grab an independent DNA sample and the try to amplify from independent sample and the sample that was sequenced.

[jigarnt]

Hi, The chances of contamination are highly unlikely because it showed up as a distinct band everytime I isolated the DNA from the same sample but different isolates grown in different plates. It was after its occurence everytime we decided to illumina sequence it. Our first guess was that it is a plasmid but the coverage which we got after assembly dosent support the notion that it could be a Plasmid. Isn't the chances of contamination ruled out if I gel extracted that band and illumina sequenced it ?

Answer 1

[jotan]

Seems highly unlikely to me. The enzymes for library preps would be incompatible with RNA.

Answer 2

[rbagnall]

My though would be no, because you would need reverse transcriptase to make cDNA prior to the DNA polymerase-directed bridge amplification.