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Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment

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ABSTRACT

Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture.

No MeSH data available.


Clustering of 10 Xanthomonas oryzae pv. oryzae strains from the Philippines based on the distribution of effector genes.Shaded blocks represent the presence of specific transcription activator-like effectors (TALEs) or Xanthomonas outer proteins (Xops) with darker grays indicating allelic variants (see Supplementary Table S4). TALE families (TEFs) and Xops are denoted at the bottom. Core (c), dispensable (d), and unique (u) effectors are highlighted at the top. Lineages are distinguished by color.
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f3: Clustering of 10 Xanthomonas oryzae pv. oryzae strains from the Philippines based on the distribution of effector genes.Shaded blocks represent the presence of specific transcription activator-like effectors (TALEs) or Xanthomonas outer proteins (Xops) with darker grays indicating allelic variants (see Supplementary Table S4). TALE families (TEFs) and Xops are denoted at the bottom. Core (c), dispensable (d), and unique (u) effectors are highlighted at the top. Lineages are distinguished by color.

Mentions: Evolutionary divergence, as a result of host selection, is a common phenomenon in plant pathogens52. To understand the composition and distribution of effector genes, we first classified all 181 TALE protein sequences, including 15 pseudogenes, into 30 TALE families (TEFs) based on RVD configuration (Supplementary Table S5). Based on this classification, each TEF displayed up to 6 alleles with half of the TEFs carrying only one allele (Supplementary Table S5). Classification using the program DisTAL, which performs alignments based on repeat sequences34, largely reveals the same groupings (Supplementary Fig. S7). We also defined a set of TEFs representing the core (20%), dispensable (60%), and unique (20%) genes (Fig. 3). Xop families were more conserved across genomes, with core and dispensable families accounting for 86% and 14%, respectively. However, Xop sequences showed 1–7 alleles per family. Interestingly, pseudogenized XopG was found only in lineage PX-A (Fig. 3).


Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment
Clustering of 10 Xanthomonas oryzae pv. oryzae strains from the Philippines based on the distribution of effector genes.Shaded blocks represent the presence of specific transcription activator-like effectors (TALEs) or Xanthomonas outer proteins (Xops) with darker grays indicating allelic variants (see Supplementary Table S4). TALE families (TEFs) and Xops are denoted at the bottom. Core (c), dispensable (d), and unique (u) effectors are highlighted at the top. Lineages are distinguished by color.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5035989&req=5

f3: Clustering of 10 Xanthomonas oryzae pv. oryzae strains from the Philippines based on the distribution of effector genes.Shaded blocks represent the presence of specific transcription activator-like effectors (TALEs) or Xanthomonas outer proteins (Xops) with darker grays indicating allelic variants (see Supplementary Table S4). TALE families (TEFs) and Xops are denoted at the bottom. Core (c), dispensable (d), and unique (u) effectors are highlighted at the top. Lineages are distinguished by color.
Mentions: Evolutionary divergence, as a result of host selection, is a common phenomenon in plant pathogens52. To understand the composition and distribution of effector genes, we first classified all 181 TALE protein sequences, including 15 pseudogenes, into 30 TALE families (TEFs) based on RVD configuration (Supplementary Table S5). Based on this classification, each TEF displayed up to 6 alleles with half of the TEFs carrying only one allele (Supplementary Table S5). Classification using the program DisTAL, which performs alignments based on repeat sequences34, largely reveals the same groupings (Supplementary Fig. S7). We also defined a set of TEFs representing the core (20%), dispensable (60%), and unique (20%) genes (Fig. 3). Xop families were more conserved across genomes, with core and dispensable families accounting for 86% and 14%, respectively. However, Xop sequences showed 1–7 alleles per family. Interestingly, pseudogenized XopG was found only in lineage PX-A (Fig. 3).

View Article: PubMed Central - PubMed

ABSTRACT

Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture.

No MeSH data available.