PMC:3091627 / 4478-6368
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091627","sourcedb":"PMC","sourceid":"3091627","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091627","text":"So far, comparative genomics involving sequenced H. pylori genomes have been limited to five clinical isolates isolated in the West and associated with gastritis [strain 26695 [20], peptic ulcers (strains J99 [GenBank:AE001439.1], P12 [EMBL:CP001217, EMBL:CP001218]), atrophic gastritis (HPAG1 [21]), or no known disease (strains G27 [22] and Shi470 [RefSeq:NC_010698]. However, no genome sequence of a H. pylori strain isolated from MALT lymphoma is currently available. Comparative genomics based on DNA-array analyses, first conducted by Salama et al. on 15 Caucasian isolates [23], led to the elucidation of the H. pylori core genome comprising the pool of ubiquitous H. pylori genes and strain-specific genes (non-ubiquitous). Gressmann et al. studied gene gain and loss during evolution, by comparing the genome of 56 globally representative strains of H. pylori; they reported that 25% of the genes were non-ubiquitous [24]. Through comparative genomics based on the analysis of 24 clinical isolates from various geographical origins (Western, Asian, African countries) using whole genome DNA arrays, we identified 213 non-ubiquitous or strain-specific genes [25]. In this study, we describe the gene distribution of these 213 non-ubiquitous genes (Additional file 1) within genomes from a large geographically homogeneous French collection of 120 well-characterized H. pylori strains associated with chronic gastritis, duodenal ulcer, intestinal metaplasia or gastric MALT lymphoma. A hierarchical clustering analysis of the DNA hybridization values identified a homogeneous phylogenic subpopulation of strains containing all of the cagPAI minus MALT lymphoma isolates. The B38 isolate was selected as a representative of this MALT lymphoma-specific cluster. Its genome sequence was completed, fully annotated, and compared with previously sequenced and published H. pylori genomes.","tracks":[{"project":"2_test","denotations":[{"id":"20537153-9252185-10781727","span":{"begin":177,"end":179},"obj":"9252185"},{"id":"20537153-16788065-10781728","span":{"begin":295,"end":297},"obj":"16788065"},{"id":"20537153-18952803-10781729","span":{"begin":335,"end":337},"obj":"18952803"},{"id":"20537153-11121067-10781730","span":{"begin":581,"end":583},"obj":"11121067"},{"id":"20537153-16217547-10781731","span":{"begin":927,"end":929},"obj":"16217547"},{"id":"20537153-18493595-10781732","span":{"begin":1167,"end":1169},"obj":"18493595"}],"attributes":[{"subj":"20537153-9252185-10781727","pred":"source","obj":"2_test"},{"subj":"20537153-16788065-10781728","pred":"source","obj":"2_test"},{"subj":"20537153-18952803-10781729","pred":"source","obj":"2_test"},{"subj":"20537153-11121067-10781730","pred":"source","obj":"2_test"},{"subj":"20537153-16217547-10781731","pred":"source","obj":"2_test"},{"subj":"20537153-18493595-10781732","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecdf93","default":true}]}]}}