Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversification
<p>Abstract</p> <p>Background</p> <p>Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of <it>Listeria monocytogenes</it>, a facultativ...
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| Format: | Article |
| Language: | English |
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BMC
2010-09-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/500 |
| _version_ | 1819086481188192256 |
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| author | Salzberg Steven L Li Zengxin Phillippy Adam M Deng Xiangyu Zhang Wei |
| author_facet | Salzberg Steven L Li Zengxin Phillippy Adam M Deng Xiangyu Zhang Wei |
| author_sort | Salzberg Steven L |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of <it>Listeria monocytogenes</it>, a facultative intracellular pathogen and the causative agent of human listeriosis, consists of at least three distinct genetic lineages. Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors.</p> <p>Results</p> <p>Here we compare the genomes of 26 <it>L. monocytogenes </it>strains representing the three lineages based on both <it>in silico </it>comparative genomic analysis and high-density, pan-genomic DNA array hybridizations. We uncover 86 genes and 8 small regulatory RNAs that likely make <it>L. monocytogenes </it>lineages differ in carbohydrate utilization and stress resistance during their residence in natural habitats and passage through the host gastrointestinal tract. We also identify 2,330 to 2,456 core genes that define this species along with an open pan-genome pool that contains more than 4,052 genes. Phylogenomic reconstructions based on 3,560 homologous groups allowed robust estimation of phylogenetic relatedness among <it>L. monocytogenes </it>strains.</p> <p>Conclusions</p> <p>Our pan-genome approach enables accurate co-analysis of DNA sequence and hybridization array data for both core gene estimation and phylogenomics. Application of our method to the pan-genome of <it>L. monocytogenes </it>sheds new insights into the intraspecific niche expansion and evolution of this important foodborne pathogen.</p> |
| first_indexed | 2024-12-21T21:20:56Z |
| format | Article |
| id | doaj.art-f4157021d1d84014b683b575837f4526 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T21:20:56Z |
| publishDate | 2010-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-f4157021d1d84014b683b575837f45262022-12-21T18:49:53ZengBMCBMC Genomics1471-21642010-09-0111150010.1186/1471-2164-11-500Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversificationSalzberg Steven LLi ZengxinPhillippy Adam MDeng XiangyuZhang Wei<p>Abstract</p> <p>Background</p> <p>Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of <it>Listeria monocytogenes</it>, a facultative intracellular pathogen and the causative agent of human listeriosis, consists of at least three distinct genetic lineages. Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors.</p> <p>Results</p> <p>Here we compare the genomes of 26 <it>L. monocytogenes </it>strains representing the three lineages based on both <it>in silico </it>comparative genomic analysis and high-density, pan-genomic DNA array hybridizations. We uncover 86 genes and 8 small regulatory RNAs that likely make <it>L. monocytogenes </it>lineages differ in carbohydrate utilization and stress resistance during their residence in natural habitats and passage through the host gastrointestinal tract. We also identify 2,330 to 2,456 core genes that define this species along with an open pan-genome pool that contains more than 4,052 genes. Phylogenomic reconstructions based on 3,560 homologous groups allowed robust estimation of phylogenetic relatedness among <it>L. monocytogenes </it>strains.</p> <p>Conclusions</p> <p>Our pan-genome approach enables accurate co-analysis of DNA sequence and hybridization array data for both core gene estimation and phylogenomics. Application of our method to the pan-genome of <it>L. monocytogenes </it>sheds new insights into the intraspecific niche expansion and evolution of this important foodborne pathogen.</p>http://www.biomedcentral.com/1471-2164/11/500 |
| spellingShingle | Salzberg Steven L Li Zengxin Phillippy Adam M Deng Xiangyu Zhang Wei Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversification BMC Genomics |
| title | Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversification |
| title_full | Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversification |
| title_fullStr | Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversification |
| title_full_unstemmed | Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversification |
| title_short | Probing the pan-genome of <it>Listeria monocytogenes</it>: new insights into intraspecific niche expansion and genomic diversification |
| title_sort | probing the pan genome of it listeria monocytogenes it new insights into intraspecific niche expansion and genomic diversification |
| url | http://www.biomedcentral.com/1471-2164/11/500 |
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