Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5
Clostridium difficile strain 630Δerm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates...
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| Veröffentlicht in: | BMC genomics 2015-01, Vol.16 (1), p.31-31, Article 31 |
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| creator | van Eijk, Erika Anvar, Seyed Yahya Browne, Hilary P Leung, Wai Yi Frank, Jeroen Schmitz, Arnoud M Roberts, Adam P Smits, Wiep Klaas |
| description | Clostridium difficile strain 630Δerm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns.
In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.
Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile. |
| doi_str_mv | 10.1186/s12864-015-1252-7 |
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In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.
Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-015-1252-7</identifier><identifier>PMID: 25636331</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Base Sequence ; Clostridium difficile - genetics ; DNA Methylation - drug effects ; Drug Resistance, Microbial - genetics ; Enterocolitis, Pseudomembranous - drug therapy ; Enterocolitis, Pseudomembranous - genetics ; Enterocolitis, Pseudomembranous - microbiology ; Erythromycin - therapeutic use ; Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences - genetics ; Translocation, Genetic</subject><ispartof>BMC genomics, 2015-01, Vol.16 (1), p.31-31, Article 31</ispartof><rights>van Eijk et al.; licensee BioMed Central. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b460t-b4f1268ba421bcf807e85f7eb0ab1f0bfd072f1c5782d71df61fde1ad6f564c13</citedby><cites>FETCH-LOGICAL-b460t-b4f1268ba421bcf807e85f7eb0ab1f0bfd072f1c5782d71df61fde1ad6f564c13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320837/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320837/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25636331$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>van Eijk, Erika</creatorcontrib><creatorcontrib>Anvar, Seyed Yahya</creatorcontrib><creatorcontrib>Browne, Hilary P</creatorcontrib><creatorcontrib>Leung, Wai Yi</creatorcontrib><creatorcontrib>Frank, Jeroen</creatorcontrib><creatorcontrib>Schmitz, Arnoud M</creatorcontrib><creatorcontrib>Roberts, Adam P</creatorcontrib><creatorcontrib>Smits, Wiep Klaas</creatorcontrib><title>Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>Clostridium difficile strain 630Δerm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns.
In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.
Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.</description><subject>Base Sequence</subject><subject>Clostridium difficile - genetics</subject><subject>DNA Methylation - drug effects</subject><subject>Drug Resistance, Microbial - genetics</subject><subject>Enterocolitis, Pseudomembranous - drug therapy</subject><subject>Enterocolitis, Pseudomembranous - genetics</subject><subject>Enterocolitis, Pseudomembranous - microbiology</subject><subject>Erythromycin - therapeutic use</subject><subject>Genome, Bacterial</subject><subject>Humans</subject><subject>Interspersed Repetitive Sequences - genetics</subject><subject>Translocation, Genetic</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1ks9uFSEUxidGY2v1AdwYli46yoEZZtyYmPFv0sRNXRNgDrcY_lxhbpO-Rx_Cp-kzyXjb5jbRDRDOx-8DvtM0L4G-ARjF2wJsFF1LoW-B9awdHjXH0A3QMhDd44P1UfOslJ-UwjCy_mlzxHrBBedw3PyeUth6XJBsMKaApOCvHUaDJFmyXCCZfCpLdrPbBTI7a51xHolXOmW1pHxFalW5SASnN9eYA8l4icqXv2LMK6oQm1M4EJ4SF43fzS5uSN2MxSejFpfinWlIenVBjwHjQqbz2D9vntiKxRe380nz4_On8-lre_b9y7fpw1mrO0GXOlpgYtSqY6CNHemAY28H1FRpsFTbmQ7MgunrT8wDzFaAnRHULGwvOgP8pHm_5253OuBsqn9WXm6zCypfyaScfFiJ7kJu0qXsOKMjHyrg4x6gXfoP4GHFpCD3ScqapFyTlCvm9e09cqqJlEUGVwx6ryKmXZEghk68A97zKoW91ORUSkZ7bwZUro3yT_yrw2fen7jrDP4HE3K_dQ</recordid><startdate>20150131</startdate><enddate>20150131</enddate><creator>van Eijk, Erika</creator><creator>Anvar, Seyed Yahya</creator><creator>Browne, Hilary P</creator><creator>Leung, Wai Yi</creator><creator>Frank, Jeroen</creator><creator>Schmitz, Arnoud M</creator><creator>Roberts, Adam P</creator><creator>Smits, Wiep Klaas</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><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>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150131</creationdate><title>Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5</title><author>van Eijk, Erika ; Anvar, Seyed Yahya ; Browne, Hilary P ; Leung, Wai Yi ; Frank, Jeroen ; Schmitz, Arnoud M ; Roberts, Adam P ; Smits, Wiep Klaas</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b460t-b4f1268ba421bcf807e85f7eb0ab1f0bfd072f1c5782d71df61fde1ad6f564c13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Base Sequence</topic><topic>Clostridium difficile - genetics</topic><topic>DNA Methylation - drug effects</topic><topic>Drug Resistance, Microbial - genetics</topic><topic>Enterocolitis, Pseudomembranous - drug therapy</topic><topic>Enterocolitis, Pseudomembranous - genetics</topic><topic>Enterocolitis, Pseudomembranous - microbiology</topic><topic>Erythromycin - therapeutic use</topic><topic>Genome, Bacterial</topic><topic>Humans</topic><topic>Interspersed Repetitive Sequences - genetics</topic><topic>Translocation, Genetic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>van Eijk, Erika</creatorcontrib><creatorcontrib>Anvar, Seyed Yahya</creatorcontrib><creatorcontrib>Browne, Hilary P</creatorcontrib><creatorcontrib>Leung, Wai Yi</creatorcontrib><creatorcontrib>Frank, Jeroen</creatorcontrib><creatorcontrib>Schmitz, Arnoud M</creatorcontrib><creatorcontrib>Roberts, Adam P</creatorcontrib><creatorcontrib>Smits, Wiep Klaas</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>van Eijk, Erika</au><au>Anvar, Seyed Yahya</au><au>Browne, Hilary P</au><au>Leung, Wai Yi</au><au>Frank, Jeroen</au><au>Schmitz, Arnoud M</au><au>Roberts, Adam P</au><au>Smits, Wiep Klaas</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2015-01-31</date><risdate>2015</risdate><volume>16</volume><issue>1</issue><spage>31</spage><epage>31</epage><pages>31-31</pages><artnum>31</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>Clostridium difficile strain 630Δerm is a spontaneous erythromycin sensitive derivative of the reference strain 630 obtained by serial passaging in antibiotic-free media. It is widely used as a defined and tractable C. difficile strain. Though largely similar to the ancestral strain, it demonstrates phenotypic differences that might be the result of underlying genetic changes. Here, we performed a de novo assembly based on single-molecule real-time sequencing and an analysis of major methylation patterns.
In addition to single nucleotide polymorphisms and various indels, we found that the mobile element CTn5 is present in the gene encoding the methyltransferase rumA rather than adhesin CD1844 where it is located in the reference strain.
Together, the genetic features identified in this study may help to explain at least part of the phenotypic differences. The annotated genome sequence of this lab strain, including the first analysis of major methylation patterns, will be a valuable resource for genetic research on C. difficile.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25636331</pmid><doi>10.1186/s12864-015-1252-7</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Base Sequence Clostridium difficile - genetics DNA Methylation - drug effects Drug Resistance, Microbial - genetics Enterocolitis, Pseudomembranous - drug therapy Enterocolitis, Pseudomembranous - genetics Enterocolitis, Pseudomembranous - microbiology Erythromycin - therapeutic use Genome, Bacterial Humans Interspersed Repetitive Sequences - genetics Translocation, Genetic |
| title | Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5 |
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