INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2015
A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and... more A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and dairy cattle manure that led to the identification of the strains AF1440T, AF1430 and AF1581, respectively. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains belonged to the genus Arcobacter and were different from all known Arcobacter species. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. The unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of strains from other Arcobacter spp. The isolates were found to be oxidase, catalase and esterase positive, and urease negative; they grew well at 30 °C under microaerophilic condition and produced NO2 and Acetoin, respectively. Based on the common origin and various physiological properties it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov., with the strains AF1440, AF1430, AF1581; type strain AF1440T (=LMG 28516T; CCUG 66485T), AF1430 (=LMG 28515; CCUG 66486) and AF1581 (=LMG 28517; CCUG 66487), respectively.
We study the small phylogeny problem in the space of multichromosomal genomes under the double cu... more We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Empirically, with chloroplast and mammalian data sets, it finds solutions as good as or better than MGR when the latter operations are prohibited. Permitting these operations allows quantitatively better solutions where part of the reconstructed ancestral genomes may be included in circular chromosomes. We discuss the biological likelihood of transpositions and block interchanges in the mammalian data.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000
We present a parameterized definition of gene clusters that allows us to control the emphasis pla... more We present a parameterized definition of gene clusters that allows us to control the emphasis placed on conserved order within a cluster. Though motivated by biological rather than mathematical considerations, this parameter turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are, and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. We infer the latter property by dynamic programming optimization of the presence of individual edges at the ancestral nodes of the phylogeny. We apply our analysis to a set of genomes drawn from the Yeast Gene Order Browser.
... Jan. 2010 Issues in the Reconstruction of Gene Order Evolution David Sankoff1, Chunfang Zheng... more ... Jan. 2010 Issues in the Reconstruction of Gene Order Evolution David Sankoff1, Chunfang Zheng2,3 (ÜËDZ), Adriana Munoz4, Zhenyu Yang1 (¨), Zaky Adam4,5, Robert Warren4, Vicky Choi6 ( á), and Qian Zhu7,8 ( ) 1 Department ...
Motivation: Some present day species have incurred a whole genome doubling event in their evoluti... more Motivation: Some present day species have incurred a whole genome doubling event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to 'halve' the genome, i.e. to reconstruct the ancestral genome at the moment of doubling, but the solution is often highly nonunique. To resolve this problem, we take account of outgroups, external reference genomes, to guide and narrow down the search. Results: We improve on a previous, computationally costly, 'brute force' method by adapting the genome halving algorithm of El-Mabrouk and Sankoff so that it rapidly and accurately constructs an ancestor close the outgroups, prior to a local optimization heuristic. We apply this to reconstruct the predoubling ancestor of Saccharomyces cerevisiae and Candida glabrata, guided by the genomes of three other yeasts that diverged before the genome doubling event. We analyze the results in terms (1) of the minimum evolution criterion, (2) how close the genome halving result is to the final (local) minimum and (3) how close the final result is to an ancestor manually constructed by an expert with access to additional information. We also visualize the set of reconstructed ancestors using classic multidimensional scaling to see what aspects of the two doubled and three unduplicated genomes influence the differences among the reconstructions. Availability: The experimental software is available on request. Contact: sankoff@uottawa.ca 1 Sequence analysis tools for dating duplication events are not pertinent to this problem since all pairs of duplicates in the doubled genome were generated at the same historical moment. 2 All cereals underwent earlier WGD event(s), but the effects of these can be filtered out on the basis of greater sequence divergence.
We introduce a way of evaluating two mathematically different optimization approaches to the same... more We introduce a way of evaluating two mathematically different optimization approaches to the same problem, namely how good or bad each is with respect to the other's criterion. We illustrate this in a comparison of breakpoint and rearrangement distances between the endpoints of a branch, where total branch-length is minimized in reconstructing ancestral genomes at the nodes of a given phylogeny. We apply this to mammalian genome evolution and simulations under various hypotheses about breakpoint re-use. Reconstructions based on rearrangement distance are superior in terms of branch length and dispersion of the multiple optimal reconstructions, but simulations show that both sets of reconstructions are equally close to the simulated ancestors.
The common intervals of two permutations on n elements are the subsets of terms contiguous in bot... more The common intervals of two permutations on n elements are the subsets of terms contiguous in both permutations. They constitute the most basic representation of conserved local order. We use d, the size of the symmetric difference (the complement of the common intervals) of the two subsets of 2({1,n}) thus determined by two permutations, as an evolutionary distance between the gene orders represented by the permutations. We consider the Steiner Tree problem in the space (2({1,n}), d) as the basis for constructing phylogenetic trees, including ancestral gene orders. We extend this to genomes with unequal gene content and to genomes containing gene families. Applied to streptophyte phylogeny, our method does not support the positioning of the complex algae Charales as a sister group to the land plants. Simulations show that the method, though unmotivated by any specific model of genome rearrangement, accurately reconstructs a tree from artificial genome data generated by random inversions deriving each genome from its ancestor on this tree.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2015
A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and... more A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and dairy cattle manure that led to the identification of the strains AF1440T, AF1430 and AF1581, respectively. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains belonged to the genus Arcobacter and were different from all known Arcobacter species. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. The unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of strains from other Arcobacter spp. The isolates were found to be oxidase, catalase and esterase positive, and urease negative; they grew well at 30 °C under microaerophilic condition and produced NO2 and Acetoin, respectively. Based on the common origin and various physiological properties it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov., with the strains AF1440, AF1430, AF1581; type strain AF1440T (=LMG 28516T; CCUG 66485T), AF1430 (=LMG 28515; CCUG 66486) and AF1581 (=LMG 28517; CCUG 66487), respectively.
The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcas... more The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcasses, is reported here. The draft genome consists of 2.2 Mbp, with a 27.12% G+C content. A total of 2,179 protein-coding genes, 46 tRNA genes, and 15 rRNAs have been identified and annotated.
Arcobacter species are members of the family Campylobacteraceae and are considered emerging enter... more Arcobacter species are members of the family Campylobacteraceae and are considered emerging enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of two Arcobacter strains isolated from human feces in an effort to provide further genetic resources for understanding the pathogenic dynamics and diversity of this important genus.
The genus Arcobacter has been associated with human illness and fecal contamination by humans and... more The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. Here, we announce the draft genome sequences of three strains of Arcobacter species cultured from pig and dairy cattle manure tanks. This information will assist in the characterization of features related to host specificities and identify potential pathogenic health risks to humans and animals.
Pseudomonas simiae 2-36, isolated from a field plot under long-term mineral fertilization, exhibi... more Pseudomonas simiae 2-36, isolated from a field plot under long-term mineral fertilization, exhibited strong in vitro antagonistic activities against Rhizoctonia solani and Gaeumannomyces graminis. We report here the draft genome sequence of Pseudomonas simiae 2-36, consisting of 6.4 Mbp with a 60.25% G؉C content and 5,790 predicted protein-coding sequences.
The genus Arcobacter has been associated with human illness and fecal contamination by humans and... more The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. Here, we announce the draft genome sequences of three strains of Arcobacter species cultured from pig and dairy cattle manure tanks. This information will assist in the characterization of features related to host specificities and identify potential pathogenic health risks to humans and animals.
The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcas... more The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcasses, is reported here. The draft genome consists of 2.2 Mbp, with a 27.12% G+C content. A total of 2,179 protein-coding genes, 46 tRNA genes, and 15 rRNAs have been identified and annotated.
Arcobacter species are members of the family Campylobacteraceae and are considered emerging enter... more Arcobacter species are members of the family Campylobacteraceae and are considered emerging enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of two Arcobacter strains isolated from human feces in an effort to provide further genetic resources for understanding the pathogenic dynamics and diversity of this important genus.
Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was recentl... more Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was recently found to cause blackleg-like symptoms on potato in the United States, Canada, and Europe. A draft genome sequence of a Canadian potato isolate of P. wasabiae CFIA1002 will enhance the characterization of its pathogenicity and host specificity features.
Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term mineral fertiliz... more Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term mineral fertilization, strongly inhibits the growth of Fusarium graminearum, Rhizoctonia solani, and Gaeumannomyces graminis. Here, we report the draft genome sequence of Pseudomonas sp. strain 2-92.
In 2014, the pathogen Clavibacter michiganensis subsp. nebraskensis was isolated from symptomatic... more In 2014, the pathogen Clavibacter michiganensis subsp. nebraskensis was isolated from symptomatic corn leaves in Manitoba, Canada. We report the draft genome sequence of C. michiganensis subsp. nebraskensis DOAB 397, consisting of 3.059 Mb with 73.0% G+C content, 2,922 predicted protein-coding sequences, 45 tRNAs, 3 rRNAs, and 37 pseudogenes.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2015
A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and... more A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and dairy cattle manure that led to the identification of the strains AF1440T, AF1430 and AF1581, respectively. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains belonged to the genus Arcobacter and were different from all known Arcobacter species. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. The unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of strains from other Arcobacter spp. The isolates were found to be oxidase, catalase and esterase positive, and urease negative; they grew well at 30 °C under microaerophilic condition and produced NO2 and Acetoin, respectively. Based on the common origin and various physiological properties it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov., with the strains AF1440, AF1430, AF1581; type strain AF1440T (=LMG 28516T; CCUG 66485T), AF1430 (=LMG 28515; CCUG 66486) and AF1581 (=LMG 28517; CCUG 66487), respectively.
We study the small phylogeny problem in the space of multichromosomal genomes under the double cu... more We study the small phylogeny problem in the space of multichromosomal genomes under the double cut and join metric. This is similar to the existing MGR (multiple genome rearrangements) approach but it allows, in addition to inversion and reciprocal translocation, operations of transposition and block interchange. Empirically, with chloroplast and mammalian data sets, it finds solutions as good as or better than MGR when the latter operations are prohibited. Permitting these operations allows quantitatively better solutions where part of the reconstructed ancestral genomes may be included in circular chromosomes. We discuss the biological likelihood of transpositions and block interchanges in the mammalian data.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000
We present a parameterized definition of gene clusters that allows us to control the emphasis pla... more We present a parameterized definition of gene clusters that allows us to control the emphasis placed on conserved order within a cluster. Though motivated by biological rather than mathematical considerations, this parameter turns out to be closely related to the bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are, and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. We infer the latter property by dynamic programming optimization of the presence of individual edges at the ancestral nodes of the phylogeny. We apply our analysis to a set of genomes drawn from the Yeast Gene Order Browser.
... Jan. 2010 Issues in the Reconstruction of Gene Order Evolution David Sankoff1, Chunfang Zheng... more ... Jan. 2010 Issues in the Reconstruction of Gene Order Evolution David Sankoff1, Chunfang Zheng2,3 (ÜËDZ), Adriana Munoz4, Zhenyu Yang1 (¨), Zaky Adam4,5, Robert Warren4, Vicky Choi6 ( á), and Qian Zhu7,8 ( ) 1 Department ...
Motivation: Some present day species have incurred a whole genome doubling event in their evoluti... more Motivation: Some present day species have incurred a whole genome doubling event in their evolutionary history, and this is reflected today in patterns of duplicated segments scattered throughout their chromosomes. These duplications may be used as data to 'halve' the genome, i.e. to reconstruct the ancestral genome at the moment of doubling, but the solution is often highly nonunique. To resolve this problem, we take account of outgroups, external reference genomes, to guide and narrow down the search. Results: We improve on a previous, computationally costly, 'brute force' method by adapting the genome halving algorithm of El-Mabrouk and Sankoff so that it rapidly and accurately constructs an ancestor close the outgroups, prior to a local optimization heuristic. We apply this to reconstruct the predoubling ancestor of Saccharomyces cerevisiae and Candida glabrata, guided by the genomes of three other yeasts that diverged before the genome doubling event. We analyze the results in terms (1) of the minimum evolution criterion, (2) how close the genome halving result is to the final (local) minimum and (3) how close the final result is to an ancestor manually constructed by an expert with access to additional information. We also visualize the set of reconstructed ancestors using classic multidimensional scaling to see what aspects of the two doubled and three unduplicated genomes influence the differences among the reconstructions. Availability: The experimental software is available on request. Contact: sankoff@uottawa.ca 1 Sequence analysis tools for dating duplication events are not pertinent to this problem since all pairs of duplicates in the doubled genome were generated at the same historical moment. 2 All cereals underwent earlier WGD event(s), but the effects of these can be filtered out on the basis of greater sequence divergence.
We introduce a way of evaluating two mathematically different optimization approaches to the same... more We introduce a way of evaluating two mathematically different optimization approaches to the same problem, namely how good or bad each is with respect to the other's criterion. We illustrate this in a comparison of breakpoint and rearrangement distances between the endpoints of a branch, where total branch-length is minimized in reconstructing ancestral genomes at the nodes of a given phylogeny. We apply this to mammalian genome evolution and simulations under various hypotheses about breakpoint re-use. Reconstructions based on rearrangement distance are superior in terms of branch length and dispersion of the multiple optimal reconstructions, but simulations show that both sets of reconstructions are equally close to the simulated ancestors.
The common intervals of two permutations on n elements are the subsets of terms contiguous in bot... more The common intervals of two permutations on n elements are the subsets of terms contiguous in both permutations. They constitute the most basic representation of conserved local order. We use d, the size of the symmetric difference (the complement of the common intervals) of the two subsets of 2({1,n}) thus determined by two permutations, as an evolutionary distance between the gene orders represented by the permutations. We consider the Steiner Tree problem in the space (2({1,n}), d) as the basis for constructing phylogenetic trees, including ancestral gene orders. We extend this to genomes with unequal gene content and to genomes containing gene families. Applied to streptophyte phylogeny, our method does not support the positioning of the complex algae Charales as a sister group to the land plants. Simulations show that the method, though unmotivated by any specific model of genome rearrangement, accurately reconstructs a tree from artificial genome data generated by random inversions deriving each genome from its ancestor on this tree.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2015
A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and... more A study was undertaken to determine the prevalence and diversity of Arcobacter species in pig and dairy cattle manure that led to the identification of the strains AF1440T, AF1430 and AF1581, respectively. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains belonged to the genus Arcobacter and were different from all known Arcobacter species. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. The unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of strains from other Arcobacter spp. The isolates were found to be oxidase, catalase and esterase positive, and urease negative; they grew well at 30 °C under microaerophilic condition and produced NO2 and Acetoin, respectively. Based on the common origin and various physiological properties it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov., with the strains AF1440, AF1430, AF1581; type strain AF1440T (=LMG 28516T; CCUG 66485T), AF1430 (=LMG 28515; CCUG 66486) and AF1581 (=LMG 28517; CCUG 66487), respectively.
The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcas... more The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcasses, is reported here. The draft genome consists of 2.2 Mbp, with a 27.12% G+C content. A total of 2,179 protein-coding genes, 46 tRNA genes, and 15 rRNAs have been identified and annotated.
Arcobacter species are members of the family Campylobacteraceae and are considered emerging enter... more Arcobacter species are members of the family Campylobacteraceae and are considered emerging enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of two Arcobacter strains isolated from human feces in an effort to provide further genetic resources for understanding the pathogenic dynamics and diversity of this important genus.
The genus Arcobacter has been associated with human illness and fecal contamination by humans and... more The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. Here, we announce the draft genome sequences of three strains of Arcobacter species cultured from pig and dairy cattle manure tanks. This information will assist in the characterization of features related to host specificities and identify potential pathogenic health risks to humans and animals.
Pseudomonas simiae 2-36, isolated from a field plot under long-term mineral fertilization, exhibi... more Pseudomonas simiae 2-36, isolated from a field plot under long-term mineral fertilization, exhibited strong in vitro antagonistic activities against Rhizoctonia solani and Gaeumannomyces graminis. We report here the draft genome sequence of Pseudomonas simiae 2-36, consisting of 6.4 Mbp with a 60.25% G؉C content and 5,790 predicted protein-coding sequences.
The genus Arcobacter has been associated with human illness and fecal contamination by humans and... more The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. Here, we announce the draft genome sequences of three strains of Arcobacter species cultured from pig and dairy cattle manure tanks. This information will assist in the characterization of features related to host specificities and identify potential pathogenic health risks to humans and animals.
The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcas... more The draft genome sequence of Arcobacter cibarius strain LMG21996(T), isolated from chicken carcasses, is reported here. The draft genome consists of 2.2 Mbp, with a 27.12% G+C content. A total of 2,179 protein-coding genes, 46 tRNA genes, and 15 rRNAs have been identified and annotated.
Arcobacter species are members of the family Campylobacteraceae and are considered emerging enter... more Arcobacter species are members of the family Campylobacteraceae and are considered emerging enteropathogens and potential zoonotic agents. Here, we report the draft genome sequences of two Arcobacter strains isolated from human feces in an effort to provide further genetic resources for understanding the pathogenic dynamics and diversity of this important genus.
Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was recentl... more Pectobacterium wasabiae, originally causing soft rot disease in horseradish in Japan, was recently found to cause blackleg-like symptoms on potato in the United States, Canada, and Europe. A draft genome sequence of a Canadian potato isolate of P. wasabiae CFIA1002 will enhance the characterization of its pathogenicity and host specificity features.
Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term mineral fertiliz... more Pseudomonas sp. strain 2-92, isolated from a Canadian field plot under long-term mineral fertilization, strongly inhibits the growth of Fusarium graminearum, Rhizoctonia solani, and Gaeumannomyces graminis. Here, we report the draft genome sequence of Pseudomonas sp. strain 2-92.
In 2014, the pathogen Clavibacter michiganensis subsp. nebraskensis was isolated from symptomatic... more In 2014, the pathogen Clavibacter michiganensis subsp. nebraskensis was isolated from symptomatic corn leaves in Manitoba, Canada. We report the draft genome sequence of C. michiganensis subsp. nebraskensis DOAB 397, consisting of 3.059 Mb with 73.0% G+C content, 2,922 predicted protein-coding sequences, 45 tRNAs, 3 rRNAs, and 37 pseudogenes.
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