In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

Jaimes-Díaz, Hueman; Larios-Serrato, Violeta; Lloret-Sánchez, Teresa; Olguín-Ruiz, Gabriela Edith; Sánchez-Vallejo, Carlos Javier; Carreño-Durán, Luis; Maldonado-Rodrı́guez, Rogelio; Méndez‐Tenorio, Alfonso

doi:10.3390/microarrays4010084

Cited by 3 publications

(2 citation statements)

References 23 publications

(29 reference statements)

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“…We should also notice that our group has published works that show the reliability of the phylogenomic classification based in Virtual Genomic Fingerprints. (Hueman et al, 2011 , 2015 ; Reyes-Prieto et al, 2011 ), and VAMPhyRE is an improved version of these earlier methods. Finally, a detailed description of the method will be submitted for publication shortly, including validation studies using both bacteria and viruses (Mendez et al, manuscript in preparation).…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway

Muñoz-Ramirez

Méndez‐Tenorio

Kato

et al. 2017

Front. Cell. Infect. Microbiol.

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Helicobacter pylori (HP) genetics may determine its clinical outcomes. Despite high prevalence of HP infection in Latin America (LA), there have been no phylogenetic studies in the region. We aimed to understand the structure of HP populations in LA mestizo individuals, where gastric cancer incidence remains high. The genome of 107 HP strains from Mexico, Nicaragua and Colombia were analyzed with 59 publicly available worldwide genomes. To study bacterial relationship on whole genome level we propose a virtual hybridization technique using thousands of high-entropy 13 bp DNA probes to generate fingerprints. Phylogenetic virtual genome fingerprint (VGF) was compared with Multi Locus Sequence Analysis (MLST) and with phylogenetic analyses of cagPAI virulence island sequences. With MLST some Nicaraguan and Mexican strains clustered close to Africa isolates, whereas European isolates were spread without clustering and intermingled with LA isolates. VGF analysis resulted in increased resolution of populations, separating European from LA strains. Furthermore, clusters with exclusively Colombian, Mexican, or Nicaraguan strains were observed, where the Colombian cluster separated from Europe, Asia, and Africa, while Nicaraguan and Mexican clades grouped close to Africa. In addition, a mixed large LA cluster including Mexican, Colombian, Nicaraguan, Peruvian, and Salvadorian strains was observed; all LA clusters separated from the Amerind clade. With cagPAI sequence analyses LA clades clearly separated from Europe, Asia and Amerind, and Colombian strains formed a single cluster. A NeighborNet analyses suggested frequent and recent recombination events particularly among LA strains. Results suggests that in the new world, H. pylori has evolved to fit mestizo LA populations, already 500 years after the Spanish colonization. This co-adaption may account for regional variability in gastric cancer risk.

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Section: Discussionmentioning

confidence: 99%

Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway

Muñoz-Ramirez

Méndez‐Tenorio

Kato

et al. 2017

Front. Cell. Infect. Microbiol.

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“…Enhancement at the initial stage of data generation is the focus of the article by Jaimes-Díaz et al [2]. The authors evaluate genomic fingerprints for Bacillus anthracis , obtained by virtual hybridization, producing patterns which simulate DNA microarrays, in order to distinguish between highly-related bacterial strains.…”

Section: Editorialmentioning

confidence: 99%

Computational Modeling and Analysis of Microarray Data: New Horizons

Ruskin

2016

Microarrays

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High-throughput microarray technologies have long been a source of data for a wide range of biomedical investigations. Over the decades, variants have been developed and sophistication of measurements has improved, with generated data providing both valuable insight and considerable analytical challenge. The cost-effectiveness of microarrays, as well as their fundamental applicability, made them a first choice for much early genomic research and efforts to improve accessibility, quality and interpretation have continued unabated. In recent years, however, the emergence of new generations of sequencing methods and, importantly, reduction of costs, has seen a preferred shift in much genomic research to the use of sequence data, both less ‘noisy’ and, arguably, with species information more directly targeted and easily interpreted. Nevertheless, new microarray data are still being generated and, together with their considerable legacy, can offer a complementary perspective on biological systems and disease pathogenesis. The challenge now is to exploit novel methods for enhancing and combining these data with those generated by alternative high-throughput techniques, such as sequencing, to provide added value. Augmentation and integration of microarray data and the new horizons this opens up, provide the theme for the papers in this Special Issue.

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Phylogenomic study and classification of mitochondrial DNA through virtual genomic fingerprints

et al. 2021

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In Silico Genomic Fingerprints of the Bacillus anthracis Group Obtained by Virtual Hybridization

Cited by 3 publications

References 23 publications

Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway

Whole Genome Sequence and Phylogenetic Analysis Show Helicobacter pylori Strains from Latin America Have Followed a Unique Evolution Pathway

Computational Modeling and Analysis of Microarray Data: New Horizons

Phylogenomic study and classification of mitochondrial DNA through virtual genomic fingerprints

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