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Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite.

McMullan M, Gardiner A, Bailey K, Kemen E, Ward BJ, Cevik V, Robert-Seilaniantz A, Schultz-Larsen T, Balmuth A, Holub E, van Oosterhout C, Jones JD - Elife (2015)

Bottom Line: Despite this divergence, their genomes are mosaic-like, with ∼25% being introgressed from other races.This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts.We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment.

View Article: PubMed Central - PubMed

Affiliation: The Sainsbury Laboratory, Norwich, United Kingdom.

ABSTRACT
How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ∼1%. Despite this divergence, their genomes are mosaic-like, with ∼25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment.

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Related in: MedlinePlus

Coverage of the reference assembly (AcNc2) by Ac2V and AcBoT.Proportion of mean coverage is a measure relative to the depth of coverage of the reference reads mapped backed to the reference assembly. The proportion of AcNc2 assembly not covered by AcBoT and/or Ac2V reads (≤10% of the mean coverage) was 3.17% (971,030 bp) in Ac2V and 4.21% (1,285,877 bp) in AcBoT.DOI:http://dx.doi.org/10.7554/eLife.04550.007
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fig2s1: Coverage of the reference assembly (AcNc2) by Ac2V and AcBoT.Proportion of mean coverage is a measure relative to the depth of coverage of the reference reads mapped backed to the reference assembly. The proportion of AcNc2 assembly not covered by AcBoT and/or Ac2V reads (≤10% of the mean coverage) was 3.17% (971,030 bp) in Ac2V and 4.21% (1,285,877 bp) in AcBoT.DOI:http://dx.doi.org/10.7554/eLife.04550.007

Mentions: To assess the overall genome-wide similarity between races, we performed alignments of reads against the AcNc2 reference assembly. For the majority of the AcNc2 genome, we observed a significant positive correlation between read depth in the reference assembly and mapping depth of the Ac2V and AcBoT reads (r = 0.65, p < 2.2e-16; Figure 2A). Some AcNc2 regions (3–4% of the assembly) showed low or zero coverage by Ac2V and/or AcBoT reads (Figure 2—figure supplement 1), suggesting the presence of highly divergent or unique regions amongst the races. These are gene sparse regions (150 and 234 genes predicted in the AcNc2, respectively), without apparent enrichment for genes encoding for secreted proteins (χ2 = 0.11, d.f. = 1, p > 0.7). Amplification of randomly selected AcNc2 genes from these regions revealed that four of the selected five genes are indeed absent/or highly diverged in the AcBoT and Ac2V races, and present in the AcNc2 genome.10.7554/eLife.04550.006Figure 2.Comparison of A. candida races using alignments of Illumina reads against the AcNc2 assembly.


Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite.

McMullan M, Gardiner A, Bailey K, Kemen E, Ward BJ, Cevik V, Robert-Seilaniantz A, Schultz-Larsen T, Balmuth A, Holub E, van Oosterhout C, Jones JD - Elife (2015)

Coverage of the reference assembly (AcNc2) by Ac2V and AcBoT.Proportion of mean coverage is a measure relative to the depth of coverage of the reference reads mapped backed to the reference assembly. The proportion of AcNc2 assembly not covered by AcBoT and/or Ac2V reads (≤10% of the mean coverage) was 3.17% (971,030 bp) in Ac2V and 4.21% (1,285,877 bp) in AcBoT.DOI:http://dx.doi.org/10.7554/eLife.04550.007
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384639&req=5

fig2s1: Coverage of the reference assembly (AcNc2) by Ac2V and AcBoT.Proportion of mean coverage is a measure relative to the depth of coverage of the reference reads mapped backed to the reference assembly. The proportion of AcNc2 assembly not covered by AcBoT and/or Ac2V reads (≤10% of the mean coverage) was 3.17% (971,030 bp) in Ac2V and 4.21% (1,285,877 bp) in AcBoT.DOI:http://dx.doi.org/10.7554/eLife.04550.007
Mentions: To assess the overall genome-wide similarity between races, we performed alignments of reads against the AcNc2 reference assembly. For the majority of the AcNc2 genome, we observed a significant positive correlation between read depth in the reference assembly and mapping depth of the Ac2V and AcBoT reads (r = 0.65, p < 2.2e-16; Figure 2A). Some AcNc2 regions (3–4% of the assembly) showed low or zero coverage by Ac2V and/or AcBoT reads (Figure 2—figure supplement 1), suggesting the presence of highly divergent or unique regions amongst the races. These are gene sparse regions (150 and 234 genes predicted in the AcNc2, respectively), without apparent enrichment for genes encoding for secreted proteins (χ2 = 0.11, d.f. = 1, p > 0.7). Amplification of randomly selected AcNc2 genes from these regions revealed that four of the selected five genes are indeed absent/or highly diverged in the AcBoT and Ac2V races, and present in the AcNc2 genome.10.7554/eLife.04550.006Figure 2.Comparison of A. candida races using alignments of Illumina reads against the AcNc2 assembly.

Bottom Line: Despite this divergence, their genomes are mosaic-like, with ∼25% being introgressed from other races.This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts.We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment.

View Article: PubMed Central - PubMed

Affiliation: The Sainsbury Laboratory, Norwich, United Kingdom.

ABSTRACT
How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ∼1%. Despite this divergence, their genomes are mosaic-like, with ∼25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment.

Show MeSH
Related in: MedlinePlus