A Novel Interpretation of Structural Dot Plots of Genomes Derived from the Analysis of Two Strains of Neisseria meningitidis
Neisseria meningitidis is the agent of invasive meningococcal disease, including cerebral meningitis and septicemia. Because the diseases caused by different clonal groups (sequence types) have their own epidemiological characteristics, it is important to understand the differences among the genomes...
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| Veröffentlicht in: | Genomics, proteomics & bioinformatics proteomics & bioinformatics, 2010-09, Vol.8 (3), p.159-169 |
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| creator | Cuff, Wilfred R. Duvvuri, Venkata R.S.K. Liang, Binhua Duvvuri, Bhargavi Wu, Gillian E. Wu, Jianhong Tsang, Raymond S.W. |
| description | Neisseria meningitidis is the agent of invasive meningococcal disease, including cerebral meningitis and septicemia. Because the diseases caused by different clonal groups (sequence types) have their own epidemiological characteristics, it is important to understand the differences among the genomes of the N. meningitidis clonal groups. To this end, a novel interpretation of a structural dot plot of genomes was devised and applied; exact nucleotide matches between the genomes of N. meningitidis serogroup A strain Z2491 and serogroup B strain MC58 were identified, leading to the specification of various structural regions. Known and putative virulence genes for each N. meningitidis strain were then classified into these regions. We found that virulence genes of MC58 tend more to the translocated regions (chromosomal segments in new sequence contexts) than do those of Z2491, notably tending towards the interface between one of the translocated regions and the collinear region. Within the collinear region, virulence genes tend to occur within 16kb of gaps in the exact matches. Verification of these tendencies using genes clustered in the cps locus was sufficiently supportive to suggest that these tendencies can be used to focus the search for and understanding of virulence genes and mechanisms of pathogenicity in these two organisms. |
| doi_str_mv | 10.1016/S1672-0229(10)60018-6 |
| format | Article |
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Because the diseases caused by different clonal groups (sequence types) have their own epidemiological characteristics, it is important to understand the differences among the genomes of the N. meningitidis clonal groups. To this end, a novel interpretation of a structural dot plot of genomes was devised and applied; exact nucleotide matches between the genomes of N. meningitidis serogroup A strain Z2491 and serogroup B strain MC58 were identified, leading to the specification of various structural regions. Known and putative virulence genes for each N. meningitidis strain were then classified into these regions. We found that virulence genes of MC58 tend more to the translocated regions (chromosomal segments in new sequence contexts) than do those of Z2491, notably tending towards the interface between one of the translocated regions and the collinear region. Within the collinear region, virulence genes tend to occur within 16kb of gaps in the exact matches. Verification of these tendencies using genes clustered in the cps locus was sufficiently supportive to suggest that these tendencies can be used to focus the search for and understanding of virulence genes and mechanisms of pathogenicity in these two organisms.</description><identifier>ISSN: 1672-0229</identifier><identifier>EISSN: 2210-3244</identifier><identifier>DOI: 10.1016/S1672-0229(10)60018-6</identifier><identifier>PMID: 20970744</identifier><language>eng</language><publisher>China: Elsevier Ltd</publisher><subject>Computational Biology - methods ; Genome, Bacterial ; Genomics - methods ; match regions ; Meningococcal Infections - microbiology ; Models, Genetic ; Multigene Family ; MUMmer ; Neisseria meningitidis ; Neisseria meningitidis - metabolism ; Phenotype ; Polymorphism, Genetic ; Proteomics - methods ; Software ; structural dot plots ; translocation ; Translocation, Genetic ; Virulence ; virulence genes</subject><ispartof>Genomics, proteomics & bioinformatics, 2010-09, Vol.8 (3), p.159-169</ispartof><rights>2010 Beijing Institute of Genomics</rights><rights>Copyright © 2010 Beijing Genomics Institute. Published by Elsevier Ltd. All rights reserved.</rights><rights>Copyright © Wanfang Data Co. Ltd. All Rights Reserved.</rights><rights>2010 Beijing Institute of Genomics 2010</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c4033-b926a74f87d142f1b7ec6ce5095de66dfdb53c2183a2bf2d885ac536d05b44cb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.wanfangdata.com.cn/images/PeriodicalImages/jyzdbzzyswxxxb-e/jyzdbzzyswxxxb-e.jpg</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054114/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S1672022910600186$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,3537,27901,27902,53766,53768,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20970744$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Cuff, Wilfred R.</creatorcontrib><creatorcontrib>Duvvuri, Venkata R.S.K.</creatorcontrib><creatorcontrib>Liang, Binhua</creatorcontrib><creatorcontrib>Duvvuri, Bhargavi</creatorcontrib><creatorcontrib>Wu, Gillian E.</creatorcontrib><creatorcontrib>Wu, Jianhong</creatorcontrib><creatorcontrib>Tsang, Raymond S.W.</creatorcontrib><title>A Novel Interpretation of Structural Dot Plots of Genomes Derived from the Analysis of Two Strains of Neisseria meningitidis</title><title>Genomics, proteomics & bioinformatics</title><addtitle>Genomics Proteomics Bioinformatics</addtitle><description>Neisseria meningitidis is the agent of invasive meningococcal disease, including cerebral meningitis and septicemia. Because the diseases caused by different clonal groups (sequence types) have their own epidemiological characteristics, it is important to understand the differences among the genomes of the N. meningitidis clonal groups. To this end, a novel interpretation of a structural dot plot of genomes was devised and applied; exact nucleotide matches between the genomes of N. meningitidis serogroup A strain Z2491 and serogroup B strain MC58 were identified, leading to the specification of various structural regions. Known and putative virulence genes for each N. meningitidis strain were then classified into these regions. We found that virulence genes of MC58 tend more to the translocated regions (chromosomal segments in new sequence contexts) than do those of Z2491, notably tending towards the interface between one of the translocated regions and the collinear region. Within the collinear region, virulence genes tend to occur within 16kb of gaps in the exact matches. Verification of these tendencies using genes clustered in the cps locus was sufficiently supportive to suggest that these tendencies can be used to focus the search for and understanding of virulence genes and mechanisms of pathogenicity in these two organisms.</description><subject>Computational Biology - methods</subject><subject>Genome, Bacterial</subject><subject>Genomics - methods</subject><subject>match regions</subject><subject>Meningococcal Infections - microbiology</subject><subject>Models, Genetic</subject><subject>Multigene Family</subject><subject>MUMmer</subject><subject>Neisseria meningitidis</subject><subject>Neisseria meningitidis - metabolism</subject><subject>Phenotype</subject><subject>Polymorphism, Genetic</subject><subject>Proteomics - methods</subject><subject>Software</subject><subject>structural dot plots</subject><subject>translocation</subject><subject>Translocation, Genetic</subject><subject>Virulence</subject><subject>virulence genes</subject><issn>1672-0229</issn><issn>2210-3244</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1v1DAQhiMEokvhJ4B8Aw4B27GT7AW0akupVBWklrPl2JOtV4m9tZ39Un88zm5ZwQnJkuWZZ96Z8Ztlbwn-RDApP9-SsqI5pnT6geCPJcakzstn2YRSgvOCMvY8mxyRk-xVCAuMGWeMvMxOKJ5WuGJskj3O0I1bQYeubAS_9BBlNM4i16Lb6AcVBy87dO4i-tm5GMb4JVjXQ0Dn4M0KNGq961G8BzSzstsGs4fu1m4UkMbunzdgQki8RD1YY-cmGm3C6-xFK7sAb57u0-zXt4u7s-_59Y_Lq7PZda4YLoq8mdJSVqytK00YbUlTgSoVcDzlGspSt7rhhaKkLiRtWqrrmkvFi1Jj3jCmmuI0-3LQXQ5ND1qBTZN1YulNL_1WOGnEvxlr7sXcrQTHnBHCkgA5CKylbaWdi4UbfNo2iMV2p5vdbhvWm82mEUAxwbhIJ9W8f2rq3cMAIYreBAVdJy24IYiacF5UaehE8gOpvAvBQ3ucjGAxmi32ZovRyTG0N1uUqe7d32sdq_64m4CvBwDS564MeBGUAatAGw8qCu3Mf1r8BhsSvLk</recordid><startdate>201009</startdate><enddate>201009</enddate><creator>Cuff, Wilfred R.</creator><creator>Duvvuri, Venkata R.S.K.</creator><creator>Liang, Binhua</creator><creator>Duvvuri, Bhargavi</creator><creator>Wu, Gillian E.</creator><creator>Wu, Jianhong</creator><creator>Tsang, Raymond S.W.</creator><general>Elsevier Ltd</general><general>Department of Mathematics and Statistics,York University,Toronto,Canada</general><general>School of Kinesiology and Health Sciences,York University,Toronto,Canada%Center for Disease Modelling,York Institute for Health Research,York University,Toronto,Canada</general><general>Public Health Agency of Canada,Canadian Science Centre for Human and Animal Health,Winnipeg,Canada%Center for Disease Modelling,York Institute for Health Research,York University,Toronto,Canada</general><general>Department of Biology,York University,Toronto,Canada%Department of Medical Microbiology,University of Manitoba,Winnipeg,Canada%School of Kinesiology and Health Sciences,York University,Toronto,Canada%Department of Biology,York University,Toronto,Canada</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>2B.</scope><scope>4A8</scope><scope>92I</scope><scope>93N</scope><scope>PSX</scope><scope>TCJ</scope><scope>5PM</scope></search><sort><creationdate>201009</creationdate><title>A Novel Interpretation of Structural Dot Plots of Genomes Derived from the Analysis of Two Strains of Neisseria meningitidis</title><author>Cuff, Wilfred R. ; 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Because the diseases caused by different clonal groups (sequence types) have their own epidemiological characteristics, it is important to understand the differences among the genomes of the N. meningitidis clonal groups. To this end, a novel interpretation of a structural dot plot of genomes was devised and applied; exact nucleotide matches between the genomes of N. meningitidis serogroup A strain Z2491 and serogroup B strain MC58 were identified, leading to the specification of various structural regions. Known and putative virulence genes for each N. meningitidis strain were then classified into these regions. We found that virulence genes of MC58 tend more to the translocated regions (chromosomal segments in new sequence contexts) than do those of Z2491, notably tending towards the interface between one of the translocated regions and the collinear region. Within the collinear region, virulence genes tend to occur within 16kb of gaps in the exact matches. Verification of these tendencies using genes clustered in the cps locus was sufficiently supportive to suggest that these tendencies can be used to focus the search for and understanding of virulence genes and mechanisms of pathogenicity in these two organisms.</abstract><cop>China</cop><pub>Elsevier Ltd</pub><pmid>20970744</pmid><doi>10.1016/S1672-0229(10)60018-6</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; Elsevier ScienceDirect Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Computational Biology - methods Genome, Bacterial Genomics - methods match regions Meningococcal Infections - microbiology Models, Genetic Multigene Family MUMmer Neisseria meningitidis Neisseria meningitidis - metabolism Phenotype Polymorphism, Genetic Proteomics - methods Software structural dot plots translocation Translocation, Genetic Virulence virulence genes |
| title | A Novel Interpretation of Structural Dot Plots of Genomes Derived from the Analysis of Two Strains of Neisseria meningitidis |
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