dc.contributor.author | Ashrafi, Roghaieh | |
dc.contributor.author | Pulkkinen, Katja | |
dc.contributor.author | Sundberg, Lotta-Riina | |
dc.contributor.author | Pekkala, Nina | |
dc.contributor.author | Ketola, Tarmo | |
dc.date.accessioned | 2015-11-16T07:40:52Z | |
dc.date.available | 2015-11-16T07:40:52Z | |
dc.date.issued | 2015 | |
dc.identifier.citation | Ashrafi, R., Pulkkinen, K., Sundberg, L.-R., Pekkala, N., & Ketola, T. (2015). A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates. <i>BMC Microbiology</i>, <i>15</i>, Article 243. <a href="https://doi.org/10.1186/s12866-015-0576-4" target="_blank">https://doi.org/10.1186/s12866-015-0576-4</a> | |
dc.identifier.other | CONVID_25283103 | |
dc.identifier.other | TUTKAID_67725 | |
dc.identifier.uri | https://jyx.jyu.fi/handle/123456789/47679 | |
dc.description.abstract | Background: Columnaris disease caused by Flavobacterium columnare is a serious problem in aquaculture, annually causing large economic losses around the world. Despite considerable research, the molecular epidemiology of F. columnare remains poorly understood.
Methods: We investigated the population structure and spatiotemporal changes in the genetic diversity of F. columnare population in Finland by using a multilocus sequence typing (MLST) and analysis (MLSA) based on DNA sequence variation within six housekeeping genes. A total of 83 strains of F. columnare were collected from eight different areas located across the country between 2003 and 2012.
Results: Partial sequencing of six housekeeping genes (trpB, tuf, atpA, rpoD, gyrB and dnaK) revealed eight sequence types and a moderate level of genetic diversity (H = 0.460). Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 3,509 nucleotides) formed two lineages, which could be further divided into five clusters. All analysed F. columnare strains appeared to have a genetic origin distinct from that of another important fish pathogen form the genus Flavobacterium, F. psychrophilum. Although the value of the index of association between alleles, 0.292 (P < 0.001), supports some degree of clonality for this species in Finland, recombination has introduced molecular diversity to the population almost three times more than mutation.
Conclusion: The results suggest that Finnish F. columnare strains have an epidemic population structure followed by clonal expansion of successful genotypes. Our study with reproducible methodology and comparable results establishes a robust framework for the discrimination and phylogenetic analysis of F. columnare isolates, which will help to improve our understanding about geographic distribution and epidemiology of columnaris disease. | |
dc.language.iso | eng | |
dc.publisher | BioMed Central Ltd. | |
dc.relation.ispartofseries | BMC Microbiology | |
dc.subject.other | Flavobacterium columnare | |
dc.subject.other | MLST/MLSA scheme | |
dc.subject.other | ClonalFrame | |
dc.subject.other | recombination rate | |
dc.subject.other | clonality | |
dc.title | A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates | |
dc.type | article | |
dc.identifier.urn | URN:NBN:fi:jyu-201511123646 | |
dc.contributor.laitos | Bio- ja ympäristötieteiden laitos | fi |
dc.contributor.laitos | Department of Biological and Environmental Science | en |
dc.contributor.oppiaine | Ekologia ja evoluutiobiologia | fi |
dc.contributor.oppiaine | Solu- ja molekyylibiologia | fi |
dc.contributor.oppiaine | Akvaattiset tieteet | fi |
dc.contributor.oppiaine | Biologisten vuorovaikutusten huippututkimusyksikkö | fi |
dc.contributor.oppiaine | Ecology and Evolutionary Biology | en |
dc.contributor.oppiaine | Cell and Molecular Biology | en |
dc.contributor.oppiaine | Aquatic Sciences | en |
dc.contributor.oppiaine | Centre of Excellence in Biological Interactions Research | en |
dc.type.uri | http://purl.org/eprint/type/JournalArticle | |
dc.date.updated | 2015-11-12T16:15:03Z | |
dc.type.coar | http://purl.org/coar/resource_type/c_2df8fbb1 | |
dc.description.reviewstatus | peerReviewed | |
dc.relation.issn | 1471-2180 | |
dc.relation.numberinseries | 0 | |
dc.relation.volume | 15 | |
dc.type.version | publishedVersion | |
dc.rights.copyright | © 2015 Ashrafi et al. | |
dc.rights.accesslevel | openAccess | fi |
dc.rights.url | http://creativecommons.org/licenses/by/4.0/ | |
dc.relation.doi | 10.1186/s12866-015-0576-4 | |
dc.type.okm | A1 | |