Next-Generation Sequencing and De Novo Assembly, Genome Organization, and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates from Duodenal Ulcer Patients in India

Abstract

The prevalence of different H. pylori genotypes in various geographical regions indicates region-specific adaptations during the course of evolution. Complete genomes of H. pylori from countries with high infection burdens, such as India, have not yet been described. Herein we present genome sequences of two H. pylori strains, NAB47 and NAD1, from India. In this report, we briefly mention the sequencing and finishing approaches, genome assembly with downstream statistics, and important features of the two draft genomes, including their phylogenetic status. We believe that these genome sequences and the comparative genomics emanating thereupon will help us to clearly understand the ancestry and biology of the Indian H. pylori genotypes, and this will be helpful in solving the so-called Indian enigma, by which high infection rates do not corroborate the minuscule number of serious outcomes observed, including gastric cancer.

Phylogenomics of Colombian Helicobacter pylori isolates

“…The genomes sequenced in this study were aligned with 34 H. pylori reference strains from the National Center for Biotechnology Information (NCBI) databases using the Gegenees v2.21 tool. This tool uses an algorithm to align genomic fragments and compares them by Blastn [ 36 , 37 ]. The fragment size was 200 bp, and the sliding step size was 100 bp.…”

Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution

“…A whole genome alignment of 27 genomes of the Malaysian isolates was carried out with 43 other H. pylori genomes (draft or complete) from NCBI database using Gegenees tool ( 38 , 39 ). The tool utilizes a fragmented alignment algorithm to calculate average similarity among the compared genomes using BLASTn.…”

Comparative Genomics of a Helicobacter pylori Isolate from a Chinese Yunnan Naxi Ethnic Aborigine Suggests High Genetic Divergence and Phage Insertion

“…Especially during the last three years, there has been a dramatic increase of genomic sequences of Helicobacter pylori in the GenBank genomics database (45 complete sequences up to May 2013, when the analysis for this study began). As the rapid development of next generation sequencing technology has generated many genome sequences [ 22 – 30 ], more studies are being focused on the investigation of potential molecular mechanisms. However, only one of these complete sequences originated from China.…”