Aug 8, 2012

I gave a short presentation at the NYU CTSI Translational Research in Progress seminar this week about our sequencing work on strains of Streptococcus mutans associated with severe tooth decay in children.  We sequenced and did de novo assembly on each of 20 strains, then did an in silico subtraction to find unique genomic elements associated with health or disease.

the details are in this PDF file:

https://www.box.com/s/fbea9b1d5cdb96f07348


6 comments:

Greg said...

That's really fascinating. I'm curious to hear more about why you didn't map to a reference genome. What was the advantage of doing De Novo sequencing?

Stuart Brown said...

The goal of the project was to find unique sequences in each genome (not present in a reference). Also, we expected a high degree of genetic diversity in each strain. So we wanted independent assemblies of each.

We broke the assemblies into 500 bp fragments from each strain from diseased mouth vs a database of all genomes from health (and the reverse). We did not find any fragments common to all disease and absent from healthy strains.

Greg said...

I was also curious about the part where you created a scaffold from the contigs.

I haven't used ABySS. Do you not get a final genome out of it? Is there more work to be done after running it? What exactly did you do with the Mauve contig mover?

Stuart Brown said...

ABySS gave us sets of contigs for each genome, from 20 to 300 contigs per genome. We used MAUVE as a sanity check- to see that the contigs align well with known genomes of the same species, and not miss any substantial chunk of the known genomes. Also makes a pretty figure for the presentation and paper.

To link up the contigs into a single chromosome we would really need a large insert mate-pair library. A lot of work for 20 different strains. Not necessary for our approach.

Cliff Beall said...

This is interesting. I just came across this through Biostars, via another blog. I have been doing some similar kinds of things with periodontitis-related organisms.

It seems like the gene content of S. mutans is much more static than other Strep pneumoniae based on that paper that said it had 30% different genes in different strains.

What about looking at the protein sequence for genes involved in acid tolerance or carbohydrate metabolism? Somethings like that could have an effect on caries.

Stuart Brown said...

The paper has been submitted. Once it is accepted, we will release all of the genome sequences for the 20 strains in GenBank. Then you and anybody else can look at their favorite genes.