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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

Nucleotide sequence identities of Xap GL 1 genes vs. other lineages and pathovars. Each histogram shows the frequency distribution of sequence identity between genes from a Xap GL 1 strain (NCPPB 1680) and their closest BLASTN matches in other lineages including GL fuscans (NCPPB 1058, 1494 and 1654), lablab-associated Xap (NCPPB 2064), X. fuscans subsp. aurantifolii (ICPB 10535), X. axonopodis pv. glycines (CFBP 2526), X. axonopodis pv. citri (306) and X. axonopodis pv. manihotis (IBSBF 1411) (Da Silva et al., 2002; Moreira et al., 2010; Bart et al., 2012; Darrasse et al., 2013a). The arrowheads indicate the positions of the peaks at 100% sequence identity between GL 1 and GL fuscans.
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Figure 11: Nucleotide sequence identities of Xap GL 1 genes vs. other lineages and pathovars. Each histogram shows the frequency distribution of sequence identity between genes from a Xap GL 1 strain (NCPPB 1680) and their closest BLASTN matches in other lineages including GL fuscans (NCPPB 1058, 1494 and 1654), lablab-associated Xap (NCPPB 2064), X. fuscans subsp. aurantifolii (ICPB 10535), X. axonopodis pv. glycines (CFBP 2526), X. axonopodis pv. citri (306) and X. axonopodis pv. manihotis (IBSBF 1411) (Da Silva et al., 2002; Moreira et al., 2010; Bart et al., 2012; Darrasse et al., 2013a). The arrowheads indicate the positions of the peaks at 100% sequence identity between GL 1 and GL fuscans.

Mentions: To further investigate this phenomenon, we calculated pairwise nucleotide sequence identities for each Xap GL 1 gene vs. its closest homolog in other lineages within X. axonopodis and X. fuscans. The results are summarized in Figure 11. Pairwise sequence identities between Xap GL 1 and Xff (GL fuscans) followed a bimodal distribution with peaks at around 96% and at 100%. The peak at 100% was not observed for identities between Xap GL 1 and other lineages (X. axonopodis pv. glycines, X. axonopodis pv. citri, X. axonopodis pv. manihotis, X. fuscans subsp. Aurantifolii, and lablab-associated Xap). Table 2 lists examples of genes with 100% identity between Xap GL 1 and Xff. Essentially the same set of genes is affected in all of the Xap GL 1 strains and the alleles are more similar to alleles from pathovars citri and glycines than to manihotis. Therefore, the most parsimonious explanation is that these alleles have been acquired by the ancestors of Xap GL 1 from the fuscans lineage.


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)

Nucleotide sequence identities of Xap GL 1 genes vs. other lineages and pathovars. Each histogram shows the frequency distribution of sequence identity between genes from a Xap GL 1 strain (NCPPB 1680) and their closest BLASTN matches in other lineages including GL fuscans (NCPPB 1058, 1494 and 1654), lablab-associated Xap (NCPPB 2064), X. fuscans subsp. aurantifolii (ICPB 10535), X. axonopodis pv. glycines (CFBP 2526), X. axonopodis pv. citri (306) and X. axonopodis pv. manihotis (IBSBF 1411) (Da Silva et al., 2002; Moreira et al., 2010; Bart et al., 2012; Darrasse et al., 2013a). The arrowheads indicate the positions of the peaks at 100% sequence identity between GL 1 and GL fuscans.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4595841&req=5

Figure 11: Nucleotide sequence identities of Xap GL 1 genes vs. other lineages and pathovars. Each histogram shows the frequency distribution of sequence identity between genes from a Xap GL 1 strain (NCPPB 1680) and their closest BLASTN matches in other lineages including GL fuscans (NCPPB 1058, 1494 and 1654), lablab-associated Xap (NCPPB 2064), X. fuscans subsp. aurantifolii (ICPB 10535), X. axonopodis pv. glycines (CFBP 2526), X. axonopodis pv. citri (306) and X. axonopodis pv. manihotis (IBSBF 1411) (Da Silva et al., 2002; Moreira et al., 2010; Bart et al., 2012; Darrasse et al., 2013a). The arrowheads indicate the positions of the peaks at 100% sequence identity between GL 1 and GL fuscans.
Mentions: To further investigate this phenomenon, we calculated pairwise nucleotide sequence identities for each Xap GL 1 gene vs. its closest homolog in other lineages within X. axonopodis and X. fuscans. The results are summarized in Figure 11. Pairwise sequence identities between Xap GL 1 and Xff (GL fuscans) followed a bimodal distribution with peaks at around 96% and at 100%. The peak at 100% was not observed for identities between Xap GL 1 and other lineages (X. axonopodis pv. glycines, X. axonopodis pv. citri, X. axonopodis pv. manihotis, X. fuscans subsp. Aurantifolii, and lablab-associated Xap). Table 2 lists examples of genes with 100% identity between Xap GL 1 and Xff. Essentially the same set of genes is affected in all of the Xap GL 1 strains and the alleles are more similar to alleles from pathovars citri and glycines than to manihotis. Therefore, the most parsimonious explanation is that these alleles have been acquired by the ancestors of Xap GL 1 from the fuscans lineage.

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