Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002
Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of tec...
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| Veröffentlicht in: | BMC genomics 2016-04, Vol.17 (302), p.315-315, Article 315 |
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| creator | Mariano, Diego César Batista Sousa, Thiago de Jesus Pereira, Felipe Luiz Aburjaile, Flávia Barh, Debmalya Rocha, Flávia Pinto, Anne Cybelle Hassan, Syed Shah Saraiva, Tessália Diniz Luerce Dorella, Fernanda Alves de Carvalho, Alex Fiorini Leal, Carlos Augusto Gomes Figueiredo, Henrique César Pereira Silva, Artur Ramos, Rommel Thiago Jucá Azevedo, Vasco Ariston Carvalho |
| description | Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements.
In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions.
In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837. |
| doi_str_mv | 10.1186/s12864-016-2673-7 |
| format | Article |
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In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions.
In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-016-2673-7</identifier><identifier>PMID: 27129708</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Chromosome Mapping - methods ; Corynebacteria ; Corynebacterium pseudotuberculosis - genetics ; DNA sequencing ; DNA, Bacterial - genetics ; Gene Library ; Genetic aspects ; Genome, Bacterial ; Genomics ; Genomics - methods ; High-Throughput Nucleotide Sequencing ; Nucleotide sequencing ; Physiological aspects ; rRNA Operon - genetics ; Sequence Analysis, DNA</subject><ispartof>BMC genomics, 2016-04, Vol.17 (302), p.315-315, Article 315</ispartof><rights>COPYRIGHT 2016 BioMed Central Ltd.</rights><rights>Copyright BioMed Central 2016</rights><rights>Mariano et al. 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c528t-37f546a705e16e9db5f063411a1bec53ef0183b6ae135623242f722b1cc056033</citedby><cites>FETCH-LOGICAL-c528t-37f546a705e16e9db5f063411a1bec53ef0183b6ae135623242f722b1cc056033</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/PMC4851793/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851793/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27129708$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mariano, Diego César Batista</creatorcontrib><creatorcontrib>Sousa, Thiago de Jesus</creatorcontrib><creatorcontrib>Pereira, Felipe Luiz</creatorcontrib><creatorcontrib>Aburjaile, Flávia</creatorcontrib><creatorcontrib>Barh, Debmalya</creatorcontrib><creatorcontrib>Rocha, Flávia</creatorcontrib><creatorcontrib>Pinto, Anne Cybelle</creatorcontrib><creatorcontrib>Hassan, Syed Shah</creatorcontrib><creatorcontrib>Saraiva, Tessália Diniz Luerce</creatorcontrib><creatorcontrib>Dorella, Fernanda Alves</creatorcontrib><creatorcontrib>de Carvalho, Alex Fiorini</creatorcontrib><creatorcontrib>Leal, Carlos Augusto Gomes</creatorcontrib><creatorcontrib>Figueiredo, Henrique César Pereira</creatorcontrib><creatorcontrib>Silva, Artur</creatorcontrib><creatorcontrib>Ramos, Rommel Thiago Jucá</creatorcontrib><creatorcontrib>Azevedo, Vasco Ariston Carvalho</creatorcontrib><title>Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements.
In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions.
In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837.</description><subject>Chromosome Mapping - methods</subject><subject>Corynebacteria</subject><subject>Corynebacterium pseudotuberculosis - genetics</subject><subject>DNA sequencing</subject><subject>DNA, Bacterial - genetics</subject><subject>Gene Library</subject><subject>Genetic aspects</subject><subject>Genome, Bacterial</subject><subject>Genomics</subject><subject>Genomics - methods</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Nucleotide sequencing</subject><subject>Physiological aspects</subject><subject>rRNA Operon - genetics</subject><subject>Sequence Analysis, DNA</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNptkk9v1DAQxSMEomXhA3BBlrjAIcVjx3b2grRa8adSBVIBcbQc7yR1ldjBTlr2wmfHyy5VFyEfbNm_98YzekXxHOgZQC3fJGC1rEoKsmRS8VI9KE6hUlAykNXDe-eT4klK15SCqpl4XJwwBWypaH1a_Pp-FXosO_RhQBLGyVnTk8GMo_MdiXiDpk_EkMGl0qSEQ9NvSYPTLaIn020g8fLTKuswBp9IaMk6xK3HxtgJo5sHMiacN2GaG4x27kNyiaQpGucJUMqeFo_aXACfHfZF8e39u6_rj-XF5w_n69VFaQWrp5KrVlTSKCoQJC43jWip5BWAgQat4NhSqHkjDQIXknFWsVYx1oC1VEjK-aJ4u_cd52bAjUWf_9DrMbrBxK0OxunjF--udBdudFULUMudwauDQQw_ZkyTzhOx2PfGY5iTzpOVAmpaQUZf_oNehzn63F6mlkpktz-GB6ozPWrn25Dr2p2pXlUCOFc8N7Iozv5D5bXBwdngsXX5_kjw-kiQmQl_Tp2ZU9LnXy6PWdizNoaUIrZ38wCqdwHT-4DpHDC9C5hWWfPi_iDvFH8TxX8DSgbKrA</recordid><startdate>20160430</startdate><enddate>20160430</enddate><creator>Mariano, Diego César Batista</creator><creator>Sousa, Thiago de Jesus</creator><creator>Pereira, Felipe Luiz</creator><creator>Aburjaile, Flávia</creator><creator>Barh, Debmalya</creator><creator>Rocha, Flávia</creator><creator>Pinto, Anne Cybelle</creator><creator>Hassan, Syed Shah</creator><creator>Saraiva, Tessália Diniz Luerce</creator><creator>Dorella, Fernanda Alves</creator><creator>de Carvalho, Alex Fiorini</creator><creator>Leal, Carlos Augusto Gomes</creator><creator>Figueiredo, Henrique César Pereira</creator><creator>Silva, Artur</creator><creator>Ramos, Rommel Thiago Jucá</creator><creator>Azevedo, Vasco Ariston Carvalho</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>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20160430</creationdate><title>Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002</title><author>Mariano, Diego César Batista ; Sousa, Thiago de Jesus ; Pereira, Felipe Luiz ; Aburjaile, Flávia ; Barh, Debmalya ; Rocha, Flávia ; Pinto, Anne Cybelle ; Hassan, Syed Shah ; Saraiva, Tessália Diniz Luerce ; Dorella, Fernanda Alves ; de Carvalho, Alex Fiorini ; Leal, Carlos Augusto Gomes ; Figueiredo, Henrique César Pereira ; Silva, Artur ; Ramos, Rommel Thiago Jucá ; Azevedo, Vasco Ariston Carvalho</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c528t-37f546a705e16e9db5f063411a1bec53ef0183b6ae135623242f722b1cc056033</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Chromosome Mapping - methods</topic><topic>Corynebacteria</topic><topic>Corynebacterium pseudotuberculosis - genetics</topic><topic>DNA sequencing</topic><topic>DNA, Bacterial - genetics</topic><topic>Gene Library</topic><topic>Genetic aspects</topic><topic>Genome, Bacterial</topic><topic>Genomics</topic><topic>Genomics - methods</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Nucleotide sequencing</topic><topic>Physiological aspects</topic><topic>rRNA Operon - genetics</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mariano, Diego César Batista</creatorcontrib><creatorcontrib>Sousa, Thiago de Jesus</creatorcontrib><creatorcontrib>Pereira, Felipe Luiz</creatorcontrib><creatorcontrib>Aburjaile, Flávia</creatorcontrib><creatorcontrib>Barh, Debmalya</creatorcontrib><creatorcontrib>Rocha, Flávia</creatorcontrib><creatorcontrib>Pinto, Anne Cybelle</creatorcontrib><creatorcontrib>Hassan, Syed Shah</creatorcontrib><creatorcontrib>Saraiva, Tessália Diniz Luerce</creatorcontrib><creatorcontrib>Dorella, Fernanda Alves</creatorcontrib><creatorcontrib>de Carvalho, Alex Fiorini</creatorcontrib><creatorcontrib>Leal, Carlos Augusto Gomes</creatorcontrib><creatorcontrib>Figueiredo, Henrique César Pereira</creatorcontrib><creatorcontrib>Silva, Artur</creatorcontrib><creatorcontrib>Ramos, Rommel Thiago Jucá</creatorcontrib><creatorcontrib>Azevedo, Vasco Ariston Carvalho</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</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>Mariano, Diego César Batista</au><au>Sousa, Thiago de Jesus</au><au>Pereira, Felipe Luiz</au><au>Aburjaile, Flávia</au><au>Barh, Debmalya</au><au>Rocha, Flávia</au><au>Pinto, Anne Cybelle</au><au>Hassan, Syed Shah</au><au>Saraiva, Tessália Diniz Luerce</au><au>Dorella, Fernanda Alves</au><au>de Carvalho, Alex Fiorini</au><au>Leal, Carlos Augusto Gomes</au><au>Figueiredo, Henrique César Pereira</au><au>Silva, Artur</au><au>Ramos, Rommel Thiago Jucá</au><au>Azevedo, Vasco Ariston Carvalho</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2016-04-30</date><risdate>2016</risdate><volume>17</volume><issue>302</issue><spage>315</spage><epage>315</epage><pages>315-315</pages><artnum>315</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements.
In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions.
In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>27129708</pmid><doi>10.1186/s12864-016-2673-7</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | BMC genomics, 2016-04, Vol.17 (302), p.315-315, Article 315 |
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| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; SpringerNature Journals; PubMed Central Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Springer Nature OA/Free Journals |
| subjects | Chromosome Mapping - methods Corynebacteria Corynebacterium pseudotuberculosis - genetics DNA sequencing DNA, Bacterial - genetics Gene Library Genetic aspects Genome, Bacterial Genomics Genomics - methods High-Throughput Nucleotide Sequencing Nucleotide sequencing Physiological aspects rRNA Operon - genetics Sequence Analysis, DNA |
| title | Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002 |
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