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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

Variation in gene content within each genetic lineage. The heatmaps essentially indicate the presence or absence of each gene in each sequenced genome. To determine the breadth of coverage of a gene, the genomic raw sequence reads are aligned against a reference pan-genome using BWA-MEM (Li, 2013, 2014) and the breadth of coverage is calculated using coverageBed (Quinlan and Hall, 2010). A coverage of one indicates complete coverage of the gene by aligned genomic sequence reads, indicating presence of the gene. A coverage of zero indicates that no genomic sequence reads matched the gene, indicating that it is absent (or at least highly divergent in sequence). In each heatmap, the genomes (columns) are clustered according to gene content and the genes (rows) are clustered according to their patterns of presence and absence across the genomes. The core genome, i.e., the subset of genes that are present in all strains, is excluded from the heatmap. (A) Summarizes the pattern of presence and absence for 1188 genes in the fuscans lineage, (B) for 472 genes in lablab-associated strains and (C) for 535 genes in Xap GL 1. Note that each gene is the representative of a cluster of orthologous genes.
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Figure 7: Variation in gene content within each genetic lineage. The heatmaps essentially indicate the presence or absence of each gene in each sequenced genome. To determine the breadth of coverage of a gene, the genomic raw sequence reads are aligned against a reference pan-genome using BWA-MEM (Li, 2013, 2014) and the breadth of coverage is calculated using coverageBed (Quinlan and Hall, 2010). A coverage of one indicates complete coverage of the gene by aligned genomic sequence reads, indicating presence of the gene. A coverage of zero indicates that no genomic sequence reads matched the gene, indicating that it is absent (or at least highly divergent in sequence). In each heatmap, the genomes (columns) are clustered according to gene content and the genes (rows) are clustered according to their patterns of presence and absence across the genomes. The core genome, i.e., the subset of genes that are present in all strains, is excluded from the heatmap. (A) Summarizes the pattern of presence and absence for 1188 genes in the fuscans lineage, (B) for 472 genes in lablab-associated strains and (C) for 535 genes in Xap GL 1. Note that each gene is the representative of a cluster of orthologous genes.

Mentions: Consistent with the indications of horizontal genetic transfer described in the previous section, we observed significant variations in gene presence and absence among strains within each of the three genetic lineages (Figure 7). Within the fuscans strains, there were 1188 clusters of orthologous genes that were present in at least one strain and absent from at least one other (Figure 7A). Among the lablab-associated strains, 472 orthologous gene clusters showed presence-absence polymorphism (Figure 7B). Among GL 1, the number was 535 (Figure 7A). Clustering of genomes according to gene content is broadly congruent with phylogeny. Supplementary Tables S2–S7 list genes whose presence distinguishes between Xff, Xap GL 1 and lablab-associated strains. Additionally, the four lablab-associated strains all contain six genes that have no close homologs amongst other sequenced xanthomonads. These are predicted to encode: three hypothetical proteins (KHS05433.1, KKY05378.1, and KHS05434.1), pilus assembly protein PilW (KHS05489.1), an oxidoreductase (KHS05432.1), and an epimerase (KHS05485.1).


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)

Variation in gene content within each genetic lineage. The heatmaps essentially indicate the presence or absence of each gene in each sequenced genome. To determine the breadth of coverage of a gene, the genomic raw sequence reads are aligned against a reference pan-genome using BWA-MEM (Li, 2013, 2014) and the breadth of coverage is calculated using coverageBed (Quinlan and Hall, 2010). A coverage of one indicates complete coverage of the gene by aligned genomic sequence reads, indicating presence of the gene. A coverage of zero indicates that no genomic sequence reads matched the gene, indicating that it is absent (or at least highly divergent in sequence). In each heatmap, the genomes (columns) are clustered according to gene content and the genes (rows) are clustered according to their patterns of presence and absence across the genomes. The core genome, i.e., the subset of genes that are present in all strains, is excluded from the heatmap. (A) Summarizes the pattern of presence and absence for 1188 genes in the fuscans lineage, (B) for 472 genes in lablab-associated strains and (C) for 535 genes in Xap GL 1. Note that each gene is the representative of a cluster of orthologous genes.
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Related In: Results  -  Collection

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Show All Figures
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Figure 7: Variation in gene content within each genetic lineage. The heatmaps essentially indicate the presence or absence of each gene in each sequenced genome. To determine the breadth of coverage of a gene, the genomic raw sequence reads are aligned against a reference pan-genome using BWA-MEM (Li, 2013, 2014) and the breadth of coverage is calculated using coverageBed (Quinlan and Hall, 2010). A coverage of one indicates complete coverage of the gene by aligned genomic sequence reads, indicating presence of the gene. A coverage of zero indicates that no genomic sequence reads matched the gene, indicating that it is absent (or at least highly divergent in sequence). In each heatmap, the genomes (columns) are clustered according to gene content and the genes (rows) are clustered according to their patterns of presence and absence across the genomes. The core genome, i.e., the subset of genes that are present in all strains, is excluded from the heatmap. (A) Summarizes the pattern of presence and absence for 1188 genes in the fuscans lineage, (B) for 472 genes in lablab-associated strains and (C) for 535 genes in Xap GL 1. Note that each gene is the representative of a cluster of orthologous genes.
Mentions: Consistent with the indications of horizontal genetic transfer described in the previous section, we observed significant variations in gene presence and absence among strains within each of the three genetic lineages (Figure 7). Within the fuscans strains, there were 1188 clusters of orthologous genes that were present in at least one strain and absent from at least one other (Figure 7A). Among the lablab-associated strains, 472 orthologous gene clusters showed presence-absence polymorphism (Figure 7B). Among GL 1, the number was 535 (Figure 7A). Clustering of genomes according to gene content is broadly congruent with phylogeny. Supplementary Tables S2–S7 list genes whose presence distinguishes between Xff, Xap GL 1 and lablab-associated strains. Additionally, the four lablab-associated strains all contain six genes that have no close homologs amongst other sequenced xanthomonads. These are predicted to encode: three hypothetical proteins (KHS05433.1, KKY05378.1, and KHS05434.1), pilus assembly protein PilW (KHS05489.1), an oxidoreductase (KHS05432.1), and an epimerase (KHS05485.1).

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