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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

Genome-wide identification of single-nucleotide variations. Panel (A) shows a density plot of single-nucleotide variations paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of Xff 4834-R (Darrasse et al., 2013b) as the reference sequence. Panel (B) shows the same phylogenetic tree as in Panel (A) but with taxon labels and some clades collapsed for clarity. In addition to the 26 newly sequenced genomes, all 134 publicly available genome assemblies from X. axonopodis, X. fuscans, X. citri, and X. euvesicatoria were included.
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Figure 3: Genome-wide identification of single-nucleotide variations. Panel (A) shows a density plot of single-nucleotide variations paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of Xff 4834-R (Darrasse et al., 2013b) as the reference sequence. Panel (B) shows the same phylogenetic tree as in Panel (A) but with taxon labels and some clades collapsed for clarity. In addition to the 26 newly sequenced genomes, all 134 publicly available genome assemblies from X. axonopodis, X. fuscans, X. citri, and X. euvesicatoria were included.

Mentions: Based on six-gene MLSA alone, strains could be ascribed to one of the three genetic lineages (GL 1, GL fuscans, and GL lablab). However, genome-wide sequence comparisons provided additional resolution and revealed distinct clades (or sub-lineages) within each lineage. Figure 3A illustrates the distribution of single-nucleotide variations across the reference sequence of the chromosome of Xff 4834-R for 160 publicly available related genome sequences. Figure 3B shows a phylogenetic reconstruction of those 160 genomes based on those variants. Consistent with the MLSA results, the strains sequenced in the present study similarly fell into three clades.


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)

Genome-wide identification of single-nucleotide variations. Panel (A) shows a density plot of single-nucleotide variations paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of Xff 4834-R (Darrasse et al., 2013b) as the reference sequence. Panel (B) shows the same phylogenetic tree as in Panel (A) but with taxon labels and some clades collapsed for clarity. In addition to the 26 newly sequenced genomes, all 134 publicly available genome assemblies from X. axonopodis, X. fuscans, X. citri, and X. euvesicatoria were included.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Genome-wide identification of single-nucleotide variations. Panel (A) shows a density plot of single-nucleotide variations paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of Xff 4834-R (Darrasse et al., 2013b) as the reference sequence. Panel (B) shows the same phylogenetic tree as in Panel (A) but with taxon labels and some clades collapsed for clarity. In addition to the 26 newly sequenced genomes, all 134 publicly available genome assemblies from X. axonopodis, X. fuscans, X. citri, and X. euvesicatoria were included.
Mentions: Based on six-gene MLSA alone, strains could be ascribed to one of the three genetic lineages (GL 1, GL fuscans, and GL lablab). However, genome-wide sequence comparisons provided additional resolution and revealed distinct clades (or sub-lineages) within each lineage. Figure 3A illustrates the distribution of single-nucleotide variations across the reference sequence of the chromosome of Xff 4834-R for 160 publicly available related genome sequences. Figure 3B shows a phylogenetic reconstruction of those 160 genomes based on those variants. Consistent with the MLSA results, the strains sequenced in the present study similarly fell into three clades.

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