New Publication!
Our latest manuscript is now published in BMC Genomics!
In the article, we report the assembly and finishing of the avirulent reference genome H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. We discuss how our results change the picture of virulence attenuation and the power of SMRT sequencing for producing high-quality reference genomes.
ASM TB: Past, Present, and Future 2017
Last week, seven of us had the privilege of representing our lab and SDSU at the American Society for Microbiology Conference on Tuberculosis 2017 in the Big Apple, where we presented research, fostered new connections, and strengthened old ones with the international TB community. We learned a tremendous amount about the physiology and genetics of Mtb, as well as several novel and exciting methodologies for future studies on this deadly pathogen. Many in attendance took interest in the seven posters we presented, particularly our exposition of the areas of the genome frequently unresolved by Illumina “Hole” genome sequencing, which we term “blind spots”, presented by Tal Shmaya. We look forward to continuing with each of these projects as they develop into publications, and presenting our future findings at more conferences in the coming months and years!
Preprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in M. tuberculosis
The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of its virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. We discuss how our results change the picture of virulence attenuation and the power of SMRT sequencing for producing high-quality reference genomes.
https://doi.org/10.1101/064840
The manuscript is under review by BMC Genomics.
Recent Publications
Valafar lab has new publications! Please check them out
Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates
A Systematic Review of Mutations in Pyrazinamidase Associated with Pyrazinamide Resistance in Mycobacterium tuberculosis Clinical Isolates.
Looking back to ASM 2015
Some of the lab members in Valafar lab attended the ASM 2015 last week in New Orleans. It was great experience for the lab as people were able to catch up with the colleagues around the world and catch up with latest trend in the field of microbiology. The lab was able to share information acquired during the convention and held a meeting to discuss where to head from here. We would like to thank ASM for the great event and we look forward to going again next year.
