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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

Single-nucleotide variation among lablab-associated strains. A density plot of single-nucleotide variations is shown paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of NCPPB 557 as the reference sequence. The country and year of isolation is indicated for each bacterial strain. Two sub-lineages are indicated by coloring in blue (a single strain) and red (three strains) respectively. The geographical locations of the countries of isolation are indicated on the world maps for each of the three sub-lineages, again colored respectively in blue or red.
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Figure 5: Single-nucleotide variation among lablab-associated strains. A density plot of single-nucleotide variations is shown paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of NCPPB 557 as the reference sequence. The country and year of isolation is indicated for each bacterial strain. Two sub-lineages are indicated by coloring in blue (a single strain) and red (three strains) respectively. The geographical locations of the countries of isolation are indicated on the world maps for each of the three sub-lineages, again colored respectively in blue or red.

Mentions: Similar, intra-lineage variation can be observed for strains within the lablab-associated strains (Figure 5) and GL 1 (Figure 6). Among lablab-associated strains, those collected in Sudan between 1957 and 1965 cluster together and are distinct from NCPPB 1713, which originates from Zimbabwe in 1962. Within GL 1, there are two multi-strain sub-lineages, which are indicated in blue and green in Figure 5. The former sub-lineage spans Australia, Canada, and Tanzania. The latter sub-lineage includes strains from Hungary, Romania, and the USA. Strain NCPPB 1138 (from Zambia, 1961) is distinct from both of these. The single GL 1 strain from Lima bean (CIAT XCP123, Colombia, 1974) is distinct from all of the strains from common bean (Figure 5); however, based on MLSA alone, it is indistinguishable from the other GL 1 strains.


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)

Single-nucleotide variation among lablab-associated strains. A density plot of single-nucleotide variations is shown paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of NCPPB 557 as the reference sequence. The country and year of isolation is indicated for each bacterial strain. Two sub-lineages are indicated by coloring in blue (a single strain) and red (three strains) respectively. The geographical locations of the countries of isolation are indicated on the world maps for each of the three sub-lineages, again colored respectively in blue or red.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Single-nucleotide variation among lablab-associated strains. A density plot of single-nucleotide variations is shown paired with a phylogenetic tree, both generated using Harvest (Treangen et al., 2014) with the chromosome of NCPPB 557 as the reference sequence. The country and year of isolation is indicated for each bacterial strain. Two sub-lineages are indicated by coloring in blue (a single strain) and red (three strains) respectively. The geographical locations of the countries of isolation are indicated on the world maps for each of the three sub-lineages, again colored respectively in blue or red.
Mentions: Similar, intra-lineage variation can be observed for strains within the lablab-associated strains (Figure 5) and GL 1 (Figure 6). Among lablab-associated strains, those collected in Sudan between 1957 and 1965 cluster together and are distinct from NCPPB 1713, which originates from Zimbabwe in 1962. Within GL 1, there are two multi-strain sub-lineages, which are indicated in blue and green in Figure 5. The former sub-lineage spans Australia, Canada, and Tanzania. The latter sub-lineage includes strains from Hungary, Romania, and the USA. Strain NCPPB 1138 (from Zambia, 1961) is distinct from both of these. The single GL 1 strain from Lima bean (CIAT XCP123, Colombia, 1974) is distinct from all of the strains from common bean (Figure 5); however, based on MLSA alone, it is indistinguishable from the other GL 1 strains.

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