{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,25]],"date-time":"2024-05-25T16:32:02Z","timestamp":1716654722685},"reference-count":20,"publisher":"American Society for Microbiology","issue":"21","license":[{"start":{"date-parts":[[2012,11,1]],"date-time":"2012-11-01T00:00:00Z","timestamp":1351728000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2012,11]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The prevalence of different\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">H. pylori<\/jats:named-content>\n            genotypes in various geographical regions indicates region-specific adaptations during the course of evolution. Complete genomes of\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">H. pylori<\/jats:named-content>\n            from countries with high infection burdens, such as India, have not yet been described. Herein we present genome sequences of two\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">H. pylori<\/jats:named-content>\n            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\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">H. pylori<\/jats:named-content>\n            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.\n          <\/jats:p>","DOI":"10.1128\/jb.01371-12","type":"journal-article","created":{"date-parts":[[2012,10,8]],"date-time":"2012-10-08T16:51:12Z","timestamp":1349715072000},"page":"5963-5964","update-policy":"http:\/\/dx.doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":14,"title":["Next-Generation Sequencing and\n            <i>De Novo<\/i>\n            Assembly, Genome Organization, and Comparative Genomic Analyses of the Genomes of Two Helicobacter pylori Isolates from Duodenal Ulcer Patients in India"],"prefix":"10.1128","volume":"194","author":[{"given":"Narender","family":"Kumar","sequence":"first","affiliation":[{"name":"Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Asish K.","family":"Mukhopadhyay","sequence":"additional","affiliation":[{"name":"Division of Bacteriology, National Institute of Cholera and Enteric Diseases (Indian Council of Medical Research), Kolkata, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajashree","family":"Patra","sequence":"additional","affiliation":[{"name":"Division of Bacteriology, National Institute of Cholera and Enteric Diseases (Indian Council of Medical Research), Kolkata, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ronita","family":"De","sequence":"additional","affiliation":[{"name":"Division of Bacteriology, National Institute of Cholera and Enteric Diseases (Indian Council of Medical Research), Kolkata, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramani","family":"Baddam","sequence":"additional","affiliation":[{"name":"Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabiha","family":"Shaik","sequence":"additional","affiliation":[{"name":"Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jawed","family":"Alam","sequence":"additional","affiliation":[{"name":"Division of Bacteriology, National Institute of Cholera and Enteric Diseases (Indian Council of Medical Research), Kolkata, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suma","family":"Tiruvayipati","sequence":"additional","affiliation":[{"name":"Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India"},{"name":"Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niyaz","family":"Ahmed","sequence":"additional","affiliation":[{"name":"Pathogen Biology Laboratory, Department of Biotechnology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India"},{"name":"Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia"},{"name":"Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1159\/000329786","article-title":"Coevolution and adaptation of Helicobacter pylori and the case for \u2018functional molecular infection epidemiology.'","volume":"20","author":"Ahmed N","year":"2011","unstructured":"AhmedN . 2011. Coevolution and adaptation of Helicobacter pylori and the case for \u2018functional molecular infection epidemiology.' Med. Princ. Pract. 20: 497\u2013 503.","journal-title":"Med. Princ. Pract."},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0005831"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI38605"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.05006-11"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-75"},{"key":"e_1_3_2_7_2","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/bioinformatics\/btq683","article-title":"Scaffolding pre-assembled contigs using SSPACE","volume":"5","author":"Boetzer M","year":"2011","unstructured":"BoetzerM HenkelCV JansenHJ ButlerD PirovanoW . 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 5:578\u2013 579.","journal-title":"Bioinformatics"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/27.23.4636"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01110-10"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-8-184"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-7-191"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1080857"},{"key":"e_1_3_2_13_2","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.229202","article-title":"BLAT: the BLAST-like alignment tool","volume":"12","author":"Kent WJ","year":"2002","unstructured":"KentWJ . 2002. BLAT: the BLAST-like alignment tool. Genome Res. 12: 656\u2013 664.","journal-title":"Genome Res."},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015076"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2004-5-2-r12"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-21"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature05562"},{"key":"e_1_3_2_18_2","article-title":"Using Galaxy to perform large-scale interactive data analyses","author":"Taylor J","year":"2007","unstructured":"TaylorJ SchenckI BlankenbergD NekrutenkoA . 2007. Using Galaxy to perform large-scale interactive data analyses. Curr. Protoc. Bioinformatics Chapter 10:Unit 10.5.","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0306629101"},{"key":"e_1_3_2_20_2","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1111\/j.1469-0691.2009.02967.x","article-title":"Helicobacter pylori typing as a tool for tracking human migration","volume":"15","author":"Yamaoka Y","year":"2009","unstructured":"YamaokaY . 2009. Helicobacter pylori typing as a tool for tracking human migration. Clin. Microbiol. Infect. 15: 829\u2013 834.","journal-title":"Clin. Microbiol. Infect."},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.074492.107"}],"container-title":["Journal of Bacteriology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.01371-12","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JB.01371-12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T17:28:07Z","timestamp":1627579687000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JB.01371-12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11]]},"references-count":20,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2012,11]]}},"alternative-id":["10.1128\/JB.01371-12"],"URL":"https:\/\/doi.org\/10.1128\/jb.01371-12","relation":{},"ISSN":["0021-9193","1098-5530"],"issn-type":[{"value":"0021-9193","type":"print"},{"value":"1098-5530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,11]]},"assertion":[{"value":"2012-07-31","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-08-17","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-10-08","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}