Visualization of consensus genome structure without using a reference genome

Abstract

Background: Standard graphical tools for whole genome comparison require a reference genome. However, any reference is also subject to annotation biases and rearrangements, and may not serve as the standard except for those of extensively studied model species. To fully exploit the rapidly accumulating sequence data from the recent sequencing technologies, genome comparison without any reference has been anticipated.

Genomics of Helicobacter pylori

“…Of those, one island encoded for the TreY‐phosphorylation triad and components of type VII secretion system as well as a reverse transcriptase, which could be associated with an antibacteriophage defense mechanism. Another new method for analyzing genome plasticity was developed by Tada et al., where they, avoiding using a reference genome that would impose bias on the analysis, instead took a pan‐genome approach to visualize how genes are located in the different genomes of a comparison …”

“…Another new method for analyzing genome plasticity was developed by Tada et al, where they, avoiding using a reference genome that would impose bias on the analysis, instead took a pan-genome approach to visualize how genes are located in the different genomes of a comparison. 19 Using a whole-genome sequencing approach on 32 strains of H. pylori, Wong et al identified genes associated with biofilm formation, one of the factors influencing the effectiveness of eradication treatment, among those some cagPAI genes were found. 20 Deletion of cagA and cagPAI was demonstrated to reduce biofilm formation.…”

Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru

“…To identify differences in the bacterial genome architecture, we applied the approach proposed by Tada et al (2017) . Briefly, orthologs gene clusters were obtained by the bidirectional best hit method and used to create a consensus genome template.…”

“…FIGURE 3 | Genomic consensus of the study populations and hpEurope references. These circular views were obtained using the method developed byTada et al (2017), which creates a consensus genome that is used as a template for alignment. Each ring represents one complete genome and each block in the ring represents a genomic region.…”

Presentation_1.PPTX

“…Our results confirmed that the indigenous group is composed by a set of three well-differentiated hspAmerindlike subpopulations (SHIM, ASHA, and PUNO) that support the idea that hspAmerind-like subpopulations are present even in urbanized cities (Puno) that were affected by the Spanish FIGURE 3 | Genomic consensus of the study populations and hpEurope references. These circular views were obtained using the method developed by Tada et al (2017), which creates a consensus genome that is used as a template for alignment. Each ring represents one complete genome and each block in the ring represents a genomic region.…”