Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes
Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (...
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doaj-ce9a6f2272dc47c0b283d0ff0d8200262020-11-24T22:31:51ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-07-01810.3389/fmicb.2017.01375253708Comparative Analysis of the Flavobacterium columnare Genomovar I and II GenomesSalih Kumru0Hasan C. Tekedar1Nagihan Gulsoy2Geoffrey C. Waldbieser3Mark L. Lawrence4Attila Karsi5Department of Basic Sciences, College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, United StatesDepartment of Basic Sciences, College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, United StatesDepartment of Biology, Faculty of Art and Sciences, Marmara UniversityIstanbul, TurkeyWarmwater Aquaculture Research Unit, United States Agricultural Research Service, StonevilleMS, United StatesDepartment of Basic Sciences, College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, United StatesDepartment of Basic Sciences, College of Veterinary Medicine, Mississippi State UniversityMississippi State, MS, United StatesColumnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here, we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90.71% similar) and DNA–DNA Hybridization (42.6% similar). Genome alignment indicated the two genomes have a large number of rearrangements. However, function-based comparative genomics analysis indicated that the two strains have similar functional capabilities with 2,263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391. Both strains carry type I secretion system, type VI secretion system, and type IX secretion system. The two genomes also have similar CRISPR capacities. The F. columnare strain ATCC 49512 genome contains a higher number of insertion sequence families and phage regions, while the F. columnare strain 94-081 genome has more genomic islands and more regulatory gene capacity. Transposon mutagenesis using Tn4351 in pathogenic strain 94-081 yielded six mutants, and experimental infections of fish showed hemolysin and glycine cleavage protein mutants had 15 and 10% mortalities, respectively, while the wild-type strain caused 100% mortalities. Our comparative and mutational analysis yielded important information on classification of genomovars I and II F. columnare as well as potential virulence genes in F. columnare strain 94-081.http://journal.frontiersin.org/article/10.3389/fmicb.2017.01375/fullFlavobacterium columnaregenomovarscomparative genomicscatfishtransposon mutagenesisvirulence |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Salih Kumru Hasan C. Tekedar Nagihan Gulsoy Geoffrey C. Waldbieser Mark L. Lawrence Attila Karsi |
spellingShingle |
Salih Kumru Hasan C. Tekedar Nagihan Gulsoy Geoffrey C. Waldbieser Mark L. Lawrence Attila Karsi Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes Frontiers in Microbiology Flavobacterium columnare genomovars comparative genomics catfish transposon mutagenesis virulence |
author_facet |
Salih Kumru Hasan C. Tekedar Nagihan Gulsoy Geoffrey C. Waldbieser Mark L. Lawrence Attila Karsi |
author_sort |
Salih Kumru |
title |
Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes |
title_short |
Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes |
title_full |
Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes |
title_fullStr |
Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes |
title_full_unstemmed |
Comparative Analysis of the Flavobacterium columnare Genomovar I and II Genomes |
title_sort |
comparative analysis of the flavobacterium columnare genomovar i and ii genomes |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2017-07-01 |
description |
Columnaris disease caused by Gram-negative rod Flavobacterium columnare is one of the most common diseases of catfish. F. columnare is also a common problem in other cultured fish species worldwide. F. columnare has three major genomovars; we have sequenced a representative strain from genomovar I (ATCC 49512, which is avirulent in catfish) and genomovar II (94-081, which is highly pathogenic in catfish). Here, we present a comparative analysis of the two genomes. Interestingly, F. columnare ATCC 49512 and 94-081 meet criteria to be considered different species based on the Average Nucleotide Identity (90.71% similar) and DNA–DNA Hybridization (42.6% similar). Genome alignment indicated the two genomes have a large number of rearrangements. However, function-based comparative genomics analysis indicated that the two strains have similar functional capabilities with 2,263 conserved orthologous clusters; strain ATCC 49512 has 290 unique orthologous clusters while strain 94-081 has 391. Both strains carry type I secretion system, type VI secretion system, and type IX secretion system. The two genomes also have similar CRISPR capacities. The F. columnare strain ATCC 49512 genome contains a higher number of insertion sequence families and phage regions, while the F. columnare strain 94-081 genome has more genomic islands and more regulatory gene capacity. Transposon mutagenesis using Tn4351 in pathogenic strain 94-081 yielded six mutants, and experimental infections of fish showed hemolysin and glycine cleavage protein mutants had 15 and 10% mortalities, respectively, while the wild-type strain caused 100% mortalities. Our comparative and mutational analysis yielded important information on classification of genomovars I and II F. columnare as well as potential virulence genes in F. columnare strain 94-081. |
topic |
Flavobacterium columnare genomovars comparative genomics catfish transposon mutagenesis virulence |
url |
http://journal.frontiersin.org/article/10.3389/fmicb.2017.01375/full |
work_keys_str_mv |
AT salihkumru comparativeanalysisoftheflavobacteriumcolumnaregenomovariandiigenomes AT hasanctekedar comparativeanalysisoftheflavobacteriumcolumnaregenomovariandiigenomes AT nagihangulsoy comparativeanalysisoftheflavobacteriumcolumnaregenomovariandiigenomes AT geoffreycwaldbieser comparativeanalysisoftheflavobacteriumcolumnaregenomovariandiigenomes AT markllawrence comparativeanalysisoftheflavobacteriumcolumnaregenomovariandiigenomes AT attilakarsi comparativeanalysisoftheflavobacteriumcolumnaregenomovariandiigenomes |
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