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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

Phylogenetic positions of the three newly sequenced strains within Xanthomonas Group 1. The figure shows the evolutionary history of the gyrB gene as inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The tree with the highest log likelihood (−7358.2201) is shown. The percentage of trees in which the associated taxa clustered together is 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 219 nucleotide sequences, taken from the studies by Young and colleagues [5] and Parkinson and colleagues [6] as well as from the three newly sequenced strains. GenBank accession numbers are indicated for the sequences. However, for clarity, only the sub-tree corresponding to Group 1 is shown. The full length of each GenBank sequence entry was used for all of the Young [5] and Parkinson [6] sequences. For the sequences taken from our data, the coordinates of the subsequence are given in the parentheses, following the GenBank accession. All positions containing gaps and missing data were eliminated. There were a total of 517 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. The newly sequenced strains are indicated by black circles (●).
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f2-genes-02-01050: Phylogenetic positions of the three newly sequenced strains within Xanthomonas Group 1. The figure shows the evolutionary history of the gyrB gene as inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The tree with the highest log likelihood (−7358.2201) is shown. The percentage of trees in which the associated taxa clustered together is 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 219 nucleotide sequences, taken from the studies by Young and colleagues [5] and Parkinson and colleagues [6] as well as from the three newly sequenced strains. GenBank accession numbers are indicated for the sequences. However, for clarity, only the sub-tree corresponding to Group 1 is shown. The full length of each GenBank sequence entry was used for all of the Young [5] and Parkinson [6] sequences. For the sequences taken from our data, the coordinates of the subsequence are given in the parentheses, following the GenBank accession. All positions containing gaps and missing data were eliminated. There were a total of 517 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. The newly sequenced strains are indicated by black circles (●).

Mentions: To more precisely resolve the newly sequenced strains' positions within Xanthomonas Group 1, we performed phylogenetic analyses based on the gyrase B (gyrB) gene (Figure 2); partial sequences of gyrB are available from two studies [5,6] including many more Xanthomonas strains than those for which there are fully sequenced genomes. The sequences that we used are given in the Supplementary Files. We found that the gyrB sequence from NCPPB4393 was identical to those from strains of X. sacchari. Previously, X. sacchari was described as comprising strains isolated from diseased sugarcane [17]. Therefore, the description may need to be modified to include strains isolated from insects.


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)

Phylogenetic positions of the three newly sequenced strains within Xanthomonas Group 1. The figure shows the evolutionary history of the gyrB gene as inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The tree with the highest log likelihood (−7358.2201) is shown. The percentage of trees in which the associated taxa clustered together is 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 219 nucleotide sequences, taken from the studies by Young and colleagues [5] and Parkinson and colleagues [6] as well as from the three newly sequenced strains. GenBank accession numbers are indicated for the sequences. However, for clarity, only the sub-tree corresponding to Group 1 is shown. The full length of each GenBank sequence entry was used for all of the Young [5] and Parkinson [6] sequences. For the sequences taken from our data, the coordinates of the subsequence are given in the parentheses, following the GenBank accession. All positions containing gaps and missing data were eliminated. There were a total of 517 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. 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

f2-genes-02-01050: Phylogenetic positions of the three newly sequenced strains within Xanthomonas Group 1. The figure shows the evolutionary history of the gyrB gene as inferred by using the Maximum Likelihood method based on the Tamura-Nei model [13]. The tree with the highest log likelihood (−7358.2201) is shown. The percentage of trees in which the associated taxa clustered together is 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 219 nucleotide sequences, taken from the studies by Young and colleagues [5] and Parkinson and colleagues [6] as well as from the three newly sequenced strains. GenBank accession numbers are indicated for the sequences. However, for clarity, only the sub-tree corresponding to Group 1 is shown. The full length of each GenBank sequence entry was used for all of the Young [5] and Parkinson [6] sequences. For the sequences taken from our data, the coordinates of the subsequence are given in the parentheses, following the GenBank accession. All positions containing gaps and missing data were eliminated. There were a total of 517 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [14]. The newly sequenced strains are indicated by black circles (●).
Mentions: To more precisely resolve the newly sequenced strains' positions within Xanthomonas Group 1, we performed phylogenetic analyses based on the gyrase B (gyrB) gene (Figure 2); partial sequences of gyrB are available from two studies [5,6] including many more Xanthomonas strains than those for which there are fully sequenced genomes. The sequences that we used are given in the Supplementary Files. We found that the gyrB sequence from NCPPB4393 was identical to those from strains of X. sacchari. Previously, X. sacchari was described as comprising strains isolated from diseased sugarcane [17]. Therefore, the description may need to be modified to include strains isolated from insects.

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