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Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans.

Aritua V, Harrison J, Sapp M, Buruchara R, Smith J, Studholme DJ - Front Microbiol (2015)

Bottom Line: This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread.The strains from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines.Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.

View Article: PubMed Central - PubMed

Affiliation: International Center for Tropical Agriculture Kampala, Uganda.

ABSTRACT
Common bacterial blight is a devastating seed-borne disease of common beans that also occurs on other legume species including lablab and Lima beans. We sequenced and analyzed the genomes of 26 strains of Xanthomonas axonopodis pv. phaseoli and X. fuscans subsp. fuscans, the causative agents of this disease, collected over four decades and six continents. This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread. The bacterial strain from Lima bean fell within the previously described Genetic Lineage 1, along with the pathovar type strain (NCPPB 3035). The strains from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines. Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.

No MeSH data available.


Related in: MedlinePlus

Overview of genomic conservation among Xap and Xff. The newly sequenced genome sequences and those of previously sequenced Xff strains 4834-R (Darrasse et al., 2013b) and CFBP 4884 (Indiana et al., 2014) were aligned against the Xac 306 chromosome reference sequence (Da Silva et al., 2002) using BLASTN with an E-value threshold of 1 × 10−6. The alignments are visualized using BLAST Ring Image Generator (BRIG) (Alikhan et al., 2011). The innermost ring indicates the position on the reference chromosome. Positions covered by BLASTN alignments are indicated with a solid color; whitespace gaps represent genomic regions not covered by the BLASTN alignments. For clarity, the three genetic lineages (GL 1, lablab-associated strains and GL fuscans) are separated by repetitions of the plot of G+C content. The black circle indicates the previously reported (Darrasse et al., 2013b) absence of the flagellar gene cluster in Xff 4834-R. The solid-lined black circles indicate strain-specific genomic deletions observed in the present study.
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Figure 1: Overview of genomic conservation among Xap and Xff. The newly sequenced genome sequences and those of previously sequenced Xff strains 4834-R (Darrasse et al., 2013b) and CFBP 4884 (Indiana et al., 2014) were aligned against the Xac 306 chromosome reference sequence (Da Silva et al., 2002) using BLASTN with an E-value threshold of 1 × 10−6. The alignments are visualized using BLAST Ring Image Generator (BRIG) (Alikhan et al., 2011). The innermost ring indicates the position on the reference chromosome. Positions covered by BLASTN alignments are indicated with a solid color; whitespace gaps represent genomic regions not covered by the BLASTN alignments. For clarity, the three genetic lineages (GL 1, lablab-associated strains and GL fuscans) are separated by repetitions of the plot of G+C content. The black circle indicates the previously reported (Darrasse et al., 2013b) absence of the flagellar gene cluster in Xff 4834-R. The solid-lined black circles indicate strain-specific genomic deletions observed in the present study.

Mentions: Figure 1 shows an overview of the de novo assemblies of each sequenced Xap and Xff genome aligned against that of the X. axonopodis pv. citri 306 (Da Silva et al., 2002). See also the Supplementary Figures for genome-wide alignments of the assemblies using Mauve (Darling et al., 2004). Note that the 26 Xap and Xff genomes were assembled de novo, using SPAdes (Bankevich et al., 2012), without use of a reference sequence.


Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans.

Aritua V, Harrison J, Sapp M, Buruchara R, Smith J, Studholme DJ - Front Microbiol (2015)

Overview of genomic conservation among Xap and Xff. The newly sequenced genome sequences and those of previously sequenced Xff strains 4834-R (Darrasse et al., 2013b) and CFBP 4884 (Indiana et al., 2014) were aligned against the Xac 306 chromosome reference sequence (Da Silva et al., 2002) using BLASTN with an E-value threshold of 1 × 10−6. The alignments are visualized using BLAST Ring Image Generator (BRIG) (Alikhan et al., 2011). The innermost ring indicates the position on the reference chromosome. Positions covered by BLASTN alignments are indicated with a solid color; whitespace gaps represent genomic regions not covered by the BLASTN alignments. For clarity, the three genetic lineages (GL 1, lablab-associated strains and GL fuscans) are separated by repetitions of the plot of G+C content. The black circle indicates the previously reported (Darrasse et al., 2013b) absence of the flagellar gene cluster in Xff 4834-R. The solid-lined black circles indicate strain-specific genomic deletions observed in the present study.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595841&req=5

Figure 1: Overview of genomic conservation among Xap and Xff. The newly sequenced genome sequences and those of previously sequenced Xff strains 4834-R (Darrasse et al., 2013b) and CFBP 4884 (Indiana et al., 2014) were aligned against the Xac 306 chromosome reference sequence (Da Silva et al., 2002) using BLASTN with an E-value threshold of 1 × 10−6. The alignments are visualized using BLAST Ring Image Generator (BRIG) (Alikhan et al., 2011). The innermost ring indicates the position on the reference chromosome. Positions covered by BLASTN alignments are indicated with a solid color; whitespace gaps represent genomic regions not covered by the BLASTN alignments. For clarity, the three genetic lineages (GL 1, lablab-associated strains and GL fuscans) are separated by repetitions of the plot of G+C content. The black circle indicates the previously reported (Darrasse et al., 2013b) absence of the flagellar gene cluster in Xff 4834-R. The solid-lined black circles indicate strain-specific genomic deletions observed in the present study.
Mentions: Figure 1 shows an overview of the de novo assemblies of each sequenced Xap and Xff genome aligned against that of the X. axonopodis pv. citri 306 (Da Silva et al., 2002). See also the Supplementary Figures for genome-wide alignments of the assemblies using Mauve (Darling et al., 2004). Note that the 26 Xap and Xff genomes were assembled de novo, using SPAdes (Bankevich et al., 2012), without use of a reference sequence.

Bottom Line: This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread.The strains from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines.Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.

View Article: PubMed Central - PubMed

Affiliation: International Center for Tropical Agriculture Kampala, Uganda.

ABSTRACT
Common bacterial blight is a devastating seed-borne disease of common beans that also occurs on other legume species including lablab and Lima beans. We sequenced and analyzed the genomes of 26 strains of Xanthomonas axonopodis pv. phaseoli and X. fuscans subsp. fuscans, the causative agents of this disease, collected over four decades and six continents. This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread. The bacterial strain from Lima bean fell within the previously described Genetic Lineage 1, along with the pathovar type strain (NCPPB 3035). The strains from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines. Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.

No MeSH data available.


Related in: MedlinePlus