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Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade.

Studholme DJ, Wasukira A, Paszkiewicz K, Aritua V, Thwaites R, Smith J, Grant M - Genes (Basel) (2011)

Bottom Line: However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction.They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans.We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK. d.j.studholme@exeter.ac.uk.

ABSTRACT
We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors.

No MeSH data available.


Related in: MedlinePlus

Molecular phylogenetic anaylsis of atpD gene of newly sequenced xanthomonads by Maximum Likelihood method. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was <100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 15 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 1,373 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. The newly sequenced bacterial strains are indicated with black circles. For each nucleotide sequence, RefSeq accession numbers and coordinates are given in parentheses. The newly sequenced strains are indicated by black circles (●).
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f1-genes-02-01050: Molecular phylogenetic anaylsis of atpD gene of newly sequenced xanthomonads by Maximum Likelihood method. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was <100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 15 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 1,373 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. The newly sequenced bacterial strains are indicated with black circles. For each nucleotide sequence, RefSeq accession numbers and coordinates are given in parentheses. The newly sequenced strains are indicated by black circles (●).

Mentions: To ascertain the phylogenetic position of the three newly sequenced strains, we generated a series of phylogenetic trees based on the nucleotide sequences of house-keeping genes. We used the same set of seven genes that were used by Pieretti and colleagues [8]. For four of these genes (atpD, dnaK, groEL and recA) we were able to build trees from multiple sequence alignments using the maximum likelihood method. However, for three of the genes (efp, glnA and gyrB) we were unable to build valid multiple sequence alignments because of a lack of orthologues with detectable nucleotide sequence similarity. For example, blastn searches against the NCBI non-redundant nucleotide database, using X. albilineans gyrB (XALc_0004) as the query, yielded no significant matches in Xylella species. The phylogenetic reconstruction [13,14] based on atpD is shown in Figure 1. Phylogenetic trees based on dnaK, groEL and recA are included in the Supplementary Files. The trees for atpD, dnaK and groEL are all toplogically consistent with each other, though there is some variation in branch lengths and the precise position of X. albilineans within Group 1 is less well resolved in the atpD tree than in the others. However, analysis of the recA sequences yielded a different branching pattern in which X. albilineans falls within the Xylella fastidiosa lineage rather than within the Xanthomonas Group 1.


Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade.

Studholme DJ, Wasukira A, Paszkiewicz K, Aritua V, Thwaites R, Smith J, Grant M - Genes (Basel) (2011)

Molecular phylogenetic anaylsis of atpD gene of newly sequenced xanthomonads by Maximum Likelihood method. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was <100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 15 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 1,373 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. The newly sequenced bacterial strains are indicated with black circles. For each nucleotide sequence, RefSeq accession numbers and coordinates are given in parentheses. The newly sequenced strains are indicated by black circles (●).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927605&req=5

f1-genes-02-01050: Molecular phylogenetic anaylsis of atpD gene of newly sequenced xanthomonads by Maximum Likelihood method. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The bootstrap consensus tree inferred from 500 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was <100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 15 nucleotide sequences. Codon positions included were 1st + 2nd + 3rd + Noncoding. All positions containing gaps and missing data were eliminated. There were a total of 1,373 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. The newly sequenced bacterial strains are indicated with black circles. For each nucleotide sequence, RefSeq accession numbers and coordinates are given in parentheses. The newly sequenced strains are indicated by black circles (●).
Mentions: To ascertain the phylogenetic position of the three newly sequenced strains, we generated a series of phylogenetic trees based on the nucleotide sequences of house-keeping genes. We used the same set of seven genes that were used by Pieretti and colleagues [8]. For four of these genes (atpD, dnaK, groEL and recA) we were able to build trees from multiple sequence alignments using the maximum likelihood method. However, for three of the genes (efp, glnA and gyrB) we were unable to build valid multiple sequence alignments because of a lack of orthologues with detectable nucleotide sequence similarity. For example, blastn searches against the NCBI non-redundant nucleotide database, using X. albilineans gyrB (XALc_0004) as the query, yielded no significant matches in Xylella species. The phylogenetic reconstruction [13,14] based on atpD is shown in Figure 1. Phylogenetic trees based on dnaK, groEL and recA are included in the Supplementary Files. The trees for atpD, dnaK and groEL are all toplogically consistent with each other, though there is some variation in branch lengths and the precise position of X. albilineans within Group 1 is less well resolved in the atpD tree than in the others. However, analysis of the recA sequences yielded a different branching pattern in which X. albilineans falls within the Xylella fastidiosa lineage rather than within the Xanthomonas Group 1.

Bottom Line: However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction.They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans.We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors.

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK. d.j.studholme@exeter.ac.uk.

ABSTRACT
We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors.

No MeSH data available.


Related in: MedlinePlus