Hi dear all,
We are studying a fungal disease and we sequenced the same fungi twice, but with different extraction times. One 11 years ago and the another one this year. The strain was extracted from the same patient, same lesion. In the genomic analysis, the strains are together with a good similarity, but after the proteins prediction and orthologous analysis , they show a very large difference. How to explain? Has anyone seen something like this?
The same behavior if found to the GO terms and Cazy Enzymes
Thank you.
Kind regards.
I guess the DNA extraction methods changed- maybe the old one gave less DNA/coverage, and the new one (having more advanced reagents maybe?) gave a deeper coverage of the strain. That can explain the differences in the gene prediction.
May you provide us with more info regarding the DNA extraction methods 11 years ago and this year?
Hi Nickolas
This may be happened to the difference in environment, the method of extraction, and the kit of extraction
You can repeat the extraction two to three time, if the same results, then you can thinking about consider this results or no
these may be heipful to you
Adams, M. D., Celniker, S. E. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
Aparicio, S., Chapman, J. et al, Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310 (2002).
Blattner, F. R., Plunkett, G. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462 (1997).
Blattner, F. R., Plunkett, G. et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716 (2004).
Following up on Barak Dror answer. Which I think is the main issue (i.e different extraction coverage. 11 Years is a LONG time for technology)
Might also be related to the database you're using changing over time.
Are you using the raw data again all the way down the pipeline or just comparing fully analyzed old data to new?
Might be worth your time to take the raw (or cleaned up) data of both down the same pipeline of alignment and see if they're still the same
First, thank you sirs for the answers. I really appreciated that Barak Dror , Laith Al-Ani Muhammad Wajid Javed and Amir Nakar
I checked some information with our microbiologist based in your comments.
Maybe I expressed myself wrong. I'm sorry about that.
The first strain was isolated 11 years ago of the patient's back lesion . The strain was preserved in sterile glycerine water and stored -80°C. The DNA extraction for the sequencing occurred in the same time with the same method.
The second strain was extracted from the ear lesion. The team did the biopsy, got the specimen, then putted in SDA medium.
What do you think? Is it possible for the conserved DNA to have lost quality or characteristics due to conservation? After all both hit the genome completeness, the phylogenetic analysis, but looking at the basic functions the new extraction has more information.
About the Bioinformatics step, I did all in the same time, same pipeline. I compared the raw and the final assemblies and the genomic annotations. (Cazy, Gene Ontology, IPR, PFAM) All of them, the same behavior.
Thanks a lot!
As per my opinion Nickolas Menezes da Silva , the DNA may not lose its quality however, there may occur certain degradations due to media, storage conditions and of course, the time span (11 years).
Nickolas Menezes da Silva thanks for the clarification. 11 years in glycerol stock at -80 is not that long of a time so present this kind of difference, in my opinion. Maybe it's a mere result of different 'serovar' of the same species? I mean, how identical are they, it's been 11 years (even if it's from the same patient). Even the fact that both of the isolates came from different locations might mean different sub-isolates.
Muhammad Wajid Javed and Barak Dror Thanks a lot for you comments. It will be very helpful. Kind regards.
- Badges
- Science topic
- Similar topics
- Analytical Chemistry
- Extraction