Limits...
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

Repertoires of T3SS effectors. The heatmap indicates the proportion covered by aligned genomic sequence reads over each T3SS effector gene DNA sequence. GenBank accession numbers are given on the right side. Genomic sequence reads were aligned against the effector gene sequences using BWA-MEM. A coverage of 1.0 represents complete coverage, indicating that the gene is present in the respective genome. A coverage of 0.0 represents a complete absence of aligned sequence reads, indicating absence of the gene from the respective genome.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4595841&req=5

Figure 9: Repertoires of T3SS effectors. The heatmap indicates the proportion covered by aligned genomic sequence reads over each T3SS effector gene DNA sequence. GenBank accession numbers are given on the right side. Genomic sequence reads were aligned against the effector gene sequences using BWA-MEM. A coverage of 1.0 represents complete coverage, indicating that the gene is present in the respective genome. A coverage of 0.0 represents a complete absence of aligned sequence reads, indicating absence of the gene from the respective genome.

Mentions: Previous genome sequencing of Xff 4834-R revealed the presence of genes encoding 30 predicted effectors potentially secreted by the Hrp T3SS (Darrasse et al., 2013b). We searched for orthologs of these and other Xanthomonas T3SS effectors in the newly sequenced Xap and Xff genomes using TBLASTN (Altschul et al., 1990) to search the genome assemblies against each protein query sequence. The results are summarized in Figure 9. There is a core set of 14 effectors that is encoded in all sequenced strains of Xap and Xff : XopK, XopZ, XopR, XopV, XopE1, XopN, XopQ, XopAK, XopA, XopL, AvrBs2, and XopX. Four of these are also included in the core set of effectors conserved among 65 strains of X. axonopodis pv. manihotis (Bart et al., 2012), namely XopE1, XopL, XopN, and XopV. Several others are encoded in most but not all of the newly sequenced genomes, for example: XopC1, XfuTAL2, and XopJ5. Others appear to be limited to just one of the three lineages. For example, XopF2 is limited to lineage fuscans, XopC2 is found only in Xap GL1 and XopAI is restricted to the lablab-associated 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)

Repertoires of T3SS effectors. The heatmap indicates the proportion covered by aligned genomic sequence reads over each T3SS effector gene DNA sequence. GenBank accession numbers are given on the right side. Genomic sequence reads were aligned against the effector gene sequences using BWA-MEM. A coverage of 1.0 represents complete coverage, indicating that the gene is present in the respective genome. A coverage of 0.0 represents a complete absence of aligned sequence reads, indicating absence of the gene from the respective genome.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 9: Repertoires of T3SS effectors. The heatmap indicates the proportion covered by aligned genomic sequence reads over each T3SS effector gene DNA sequence. GenBank accession numbers are given on the right side. Genomic sequence reads were aligned against the effector gene sequences using BWA-MEM. A coverage of 1.0 represents complete coverage, indicating that the gene is present in the respective genome. A coverage of 0.0 represents a complete absence of aligned sequence reads, indicating absence of the gene from the respective genome.
Mentions: Previous genome sequencing of Xff 4834-R revealed the presence of genes encoding 30 predicted effectors potentially secreted by the Hrp T3SS (Darrasse et al., 2013b). We searched for orthologs of these and other Xanthomonas T3SS effectors in the newly sequenced Xap and Xff genomes using TBLASTN (Altschul et al., 1990) to search the genome assemblies against each protein query sequence. The results are summarized in Figure 9. There is a core set of 14 effectors that is encoded in all sequenced strains of Xap and Xff : XopK, XopZ, XopR, XopV, XopE1, XopN, XopQ, XopAK, XopA, XopL, AvrBs2, and XopX. Four of these are also included in the core set of effectors conserved among 65 strains of X. axonopodis pv. manihotis (Bart et al., 2012), namely XopE1, XopL, XopN, and XopV. Several others are encoded in most but not all of the newly sequenced genomes, for example: XopC1, XfuTAL2, and XopJ5. Others appear to be limited to just one of the three lineages. For example, XopF2 is limited to lineage fuscans, XopC2 is found only in Xap GL1 and XopAI is restricted to the lablab-associated 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