We recently performed WGS for Xanthomonas vesicatoria, isolated from Tomatoes. Having previous experience with RNAseq and Metagenomics, I thought it will be a smooth ride. We purified the colonies and then validated the identity using specie specific primers. Xvesi +ve colonies were then grown in suspension culture for DNA isolation and subsequent WGS.
However, when we assembled the genome the story was alarming. The results revealed that most reads mapped to Stentrophomonas maltophilia. Though Sten. maltophilia is classified as X. maltophilia is literature. I suspect that SOAPdenovo is playing up or we have real contamination issue.
How do we address the issue and get the right assembly?.
I would appreciate suggestions for a webserver. We used PATRIC https://www.patricbrc.org/
In this case you can troubleshoot on few things. How specific are these species specific primers? These two species are very close and belong to same family and false positives might occur in PCR. Further, isolation is tricky and sometimes its very very hard to get pure isolates. In colony based methods from plates, colonies are not always pure.
Have you checked what all/other genus/species might be present in your sample.
If you think the assembly is problem, try any other assembly method and compare the outputs.
Hi Muhammad
typiccaly, you'll get more reliable results in omics by choosing the right genome and assembly.
you can go to NCBI website and you'll get enough data to work on your favorite spicy:
https://www.ncbi.nlm.nih.gov/search/all/?term=Xanthomonas%20vesicatoria
all the best
fred