Hi,
do you know if it can happen that the plasmid sequence of a bacterium is "split" in different contigs coming from the ngs results?I have problems in trying to "foresee" the entire sequence of the plasmid and determine if I have one or more plasmids from the data I have. Should one plasmid correspond to 1 contig as a general rule?For example from my sequencing data I realize that I have different resistance genes on different contigs...but , in theory, I suppose these different genes are on the same plasmid ..Could it mean that the plasmid is spit in different contigs as a result of the sequencing technology?How can I "reconstruct" the original intact plasmid sequence?I hope to have been clear.
Thanks
Hi,
You didn't specify the technology you're using to sequence the plasmid. If it's based on short reads (
Hi,
You didn't specify the technology you're using to sequence the plasmid. If it's based on short reads (
You can use the partial sequences of the plasmid (or suspected plasmid) to find out with plasmid(s) you are dealing with (for instance, using the Plasmidfinder of DTU) and then map your reads against the reference sequence of the plasmid(s). If the mapping results in a continuous sequence, it is likely you are dealing with one continuous plasmid.
Hello Silvia,
Yes you can expect plasmid sequence covered in split contigs. As Eudora said if your plasmid is having contamination of rest of the genome, it will be difficult to separate plasmid contigs of your interest. Thus you should first map the total reads on to the nearest reference genome available to remove the bacterial genome contamination and can use its unmapped reads for assembly. It will reduce the chance of misassembly and you may get your plasmid in single scaffold.
If this approach does not solve your problem then you can design primers using partial sequence of plasmid which you obtained from assembly or nearest genome and can sequence on Sanger using primer walking approach which is the best validation step and cost effective compare to PacBio or Oxford Nanopore.
- Badges
- Science topic
- Similar topics
- Entomology
- Resistance