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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

Multi-locus sequence analysis to determine the phylogenetic positions of the sequenced strains within the species X. axonopodis and X. fuscans. The phylogenetic tree is based on alignment of six concatenated gene sequences (atpD, dnaK, efp, fyuA, glnA, and gyrB). The sequences for NCPPB 220, 301, 1138, 1420, 1646, 1680, 1811, 3035, and CIAT XCP123 were identical to those of CFBP 412, 6164, 6546, 6982, 6983, 6984, and 6985, which are classified as belonging to “pv. phaseoli GL1” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.4 (Rademaker et al., 2005). The sequences for NCPPB 381, 670, 1056, 1058, 1158, 1402, 1433, 1495, 1654, 2665, 3660, and CIAT X621 were identical to those of CFBP 1845, and 4834-R, which are classified as “pv. phaseoli GL fuscans” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.6 (Rademaker et al., 2005). The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time Reversible model (Nei and Kumar, 2000). The tree with the highest log likelihood (−17100.2449) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree (s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 284 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 2697 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al., 2013).
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Figure 2: Multi-locus sequence analysis to determine the phylogenetic positions of the sequenced strains within the species X. axonopodis and X. fuscans. The phylogenetic tree is based on alignment of six concatenated gene sequences (atpD, dnaK, efp, fyuA, glnA, and gyrB). The sequences for NCPPB 220, 301, 1138, 1420, 1646, 1680, 1811, 3035, and CIAT XCP123 were identical to those of CFBP 412, 6164, 6546, 6982, 6983, 6984, and 6985, which are classified as belonging to “pv. phaseoli GL1” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.4 (Rademaker et al., 2005). The sequences for NCPPB 381, 670, 1056, 1058, 1158, 1402, 1433, 1495, 1654, 2665, 3660, and CIAT X621 were identical to those of CFBP 1845, and 4834-R, which are classified as “pv. phaseoli GL fuscans” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.6 (Rademaker et al., 2005). The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time Reversible model (Nei and Kumar, 2000). The tree with the highest log likelihood (−17100.2449) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree (s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 284 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 2697 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al., 2013).

Mentions: To ascertain the phylogenetic positions of each sequenced strain, we initially used a multi-locus sequence analysis (MLSA) approach, using concatenated sequences from six genes that had been used in previous MLSA studies (Young et al., 2008; Almeida et al., 2010; Hajri et al., 2012; Hamza et al., 2012). This approach had the advantage that we could include in the analysis many Xap strains and other xanthomonads whose genomes had not been sequenced but for which MLSA data were available. Nucleotide sequences are available for these six genes from a large number of xanthomonads, either from whole-genome sequence assemblies or from the MLSA studies. We combined the publicly available sequences with homologous sequences extracted from the genomes newly sequenced for this study. The results of the MLSA revealed that the newly sequenced Xap and Xff genomes each fell into one of three distinct clades: GL 1, GL fuscans and a previously undescribed lineage associated with lablab bean (Figure 2).


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)

Multi-locus sequence analysis to determine the phylogenetic positions of the sequenced strains within the species X. axonopodis and X. fuscans. The phylogenetic tree is based on alignment of six concatenated gene sequences (atpD, dnaK, efp, fyuA, glnA, and gyrB). The sequences for NCPPB 220, 301, 1138, 1420, 1646, 1680, 1811, 3035, and CIAT XCP123 were identical to those of CFBP 412, 6164, 6546, 6982, 6983, 6984, and 6985, which are classified as belonging to “pv. phaseoli GL1” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.4 (Rademaker et al., 2005). The sequences for NCPPB 381, 670, 1056, 1058, 1158, 1402, 1433, 1495, 1654, 2665, 3660, and CIAT X621 were identical to those of CFBP 1845, and 4834-R, which are classified as “pv. phaseoli GL fuscans” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.6 (Rademaker et al., 2005). The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time Reversible model (Nei and Kumar, 2000). The tree with the highest log likelihood (−17100.2449) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree (s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 284 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 2697 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al., 2013).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
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Figure 2: Multi-locus sequence analysis to determine the phylogenetic positions of the sequenced strains within the species X. axonopodis and X. fuscans. The phylogenetic tree is based on alignment of six concatenated gene sequences (atpD, dnaK, efp, fyuA, glnA, and gyrB). The sequences for NCPPB 220, 301, 1138, 1420, 1646, 1680, 1811, 3035, and CIAT XCP123 were identical to those of CFBP 412, 6164, 6546, 6982, 6983, 6984, and 6985, which are classified as belonging to “pv. phaseoli GL1” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.4 (Rademaker et al., 2005). The sequences for NCPPB 381, 670, 1056, 1058, 1158, 1402, 1433, 1495, 1654, 2665, 3660, and CIAT X621 were identical to those of CFBP 1845, and 4834-R, which are classified as “pv. phaseoli GL fuscans” (Alavi et al., 2008; Mhedbi-Hajri et al., 2013) and genetic group 9.6 (Rademaker et al., 2005). The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time Reversible model (Nei and Kumar, 2000). The tree with the highest log likelihood (−17100.2449) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree (s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 284 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 2697 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al., 2013).
Mentions: To ascertain the phylogenetic positions of each sequenced strain, we initially used a multi-locus sequence analysis (MLSA) approach, using concatenated sequences from six genes that had been used in previous MLSA studies (Young et al., 2008; Almeida et al., 2010; Hajri et al., 2012; Hamza et al., 2012). This approach had the advantage that we could include in the analysis many Xap strains and other xanthomonads whose genomes had not been sequenced but for which MLSA data were available. Nucleotide sequences are available for these six genes from a large number of xanthomonads, either from whole-genome sequence assemblies or from the MLSA studies. We combined the publicly available sequences with homologous sequences extracted from the genomes newly sequenced for this study. The results of the MLSA revealed that the newly sequenced Xap and Xff genomes each fell into one of three distinct clades: GL 1, GL fuscans and a previously undescribed lineage associated with lablab bean (Figure 2).

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