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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

Alignment of the three Xanthomonas Group 1 new genome sequences against the chromosome of X. albilineans. The blue and red inner track represents annotated genes. The next three black tracks represent depth of coverage by Illumina sequence reads for NCPPB1131, NCPPB4393 and NCPPB1131 respectively. The four colored outer rings indicate sequence similarity to the genome assemblies of NCPPB1131 (olive), NCPPB4393 (yellow) and NCPPB1131 (grey) respectively.
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f3-genes-02-01050: Alignment of the three Xanthomonas Group 1 new genome sequences against the chromosome of X. albilineans. The blue and red inner track represents annotated genes. The next three black tracks represent depth of coverage by Illumina sequence reads for NCPPB1131, NCPPB4393 and NCPPB1131 respectively. The four colored outer rings indicate sequence similarity to the genome assemblies of NCPPB1131 (olive), NCPPB4393 (yellow) and NCPPB1131 (grey) respectively.

Mentions: We aligned the three genome assemblies against the genome sequence of X. albilineans species. We also aligned the reads, without performing de novo assembly. Figure 3 illustrates a genome-wide overview of these alignments. It should be noted that the sequencing depths obtained for the three strains ensures complete coverage over the entire breadth of the genomes. This means that by examining alignments of sequence reads against a reference sequence, independently from any de novo assembly, we can confidently determine the presence or absence of genes. The depths of coverage of each genome, as determined by depths of alignments of raw reads against assemblies, were 20× (NCPPB1131), 67× (NCPPB1132) and 72× (NCPPB4393).


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)

Alignment of the three Xanthomonas Group 1 new genome sequences against the chromosome of X. albilineans. The blue and red inner track represents annotated genes. The next three black tracks represent depth of coverage by Illumina sequence reads for NCPPB1131, NCPPB4393 and NCPPB1131 respectively. The four colored outer rings indicate sequence similarity to the genome assemblies of NCPPB1131 (olive), NCPPB4393 (yellow) and NCPPB1131 (grey) respectively.
© Copyright Policy
Related In: Results  -  Collection

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

f3-genes-02-01050: Alignment of the three Xanthomonas Group 1 new genome sequences against the chromosome of X. albilineans. The blue and red inner track represents annotated genes. The next three black tracks represent depth of coverage by Illumina sequence reads for NCPPB1131, NCPPB4393 and NCPPB1131 respectively. The four colored outer rings indicate sequence similarity to the genome assemblies of NCPPB1131 (olive), NCPPB4393 (yellow) and NCPPB1131 (grey) respectively.
Mentions: We aligned the three genome assemblies against the genome sequence of X. albilineans species. We also aligned the reads, without performing de novo assembly. Figure 3 illustrates a genome-wide overview of these alignments. It should be noted that the sequencing depths obtained for the three strains ensures complete coverage over the entire breadth of the genomes. This means that by examining alignments of sequence reads against a reference sequence, independently from any de novo assembly, we can confidently determine the presence or absence of genes. The depths of coverage of each genome, as determined by depths of alignments of raw reads against assemblies, were 20× (NCPPB1131), 67× (NCPPB1132) and 72× (NCPPB4393).

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