title: Paralog re-emergence: a novel, historically contingent mechanism in the evolution of antimicrobial resistance.
abstract: Evolution of resistance to drugs and pesticides poses a serious threat to human health and agricultural production. CYP51 encodes the target site of azole fungicides, widely used clinically and in agriculture. Azole resistance can evolve due to point mutations or overexpression of CYP51, and previous studies have shown that fungicide-resistant alleles have arisen by de novo mutation. Paralogs CYP51A and CYP51B are found in filamentous ascomycetes, but CYP51A has been lost from multiple lineages. Here, we show that in the barley pathogen Rhynchosporium commune, re-emergence of CYP51A constitutes a novel mechanism for the evolution of resistance to azoles. Pyrosequencing analysis of historical barley leaf samples from a unique long-term experiment from 1892 to 2008 indicates that the majority of the R. commune population lacked CYP51A until 1985, after which the frequency of CYP51A rapidly increased. Functional analysis demonstrates that CYP51A retains the same substrate as CYP51B, but with different transcriptional regulation. Phylogenetic analyses show that the origin of CYP51A far predates azole use, and newly sequenced Rhynchosporium genomes show CYP51A persisting in the R. commune lineage rather than being regained by horizontal gene transfer; therefore, CYP51A re-emergence provides an example of adaptation to novel compounds by selection from standing genetic variation.
authors.affiliation: Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
authors.forename: Nichola J
authors.initials: NJ
authors.lastname: Hawkins
authors.affiliation: Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom.
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Cools
authors.affiliation: Research Biology, Syngenta Crop Protection, Basel, Switzerland.
authors.forename: Helge
authors.initials: H
authors.lastname: Sierotzki
authors.affiliation: School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, United Kingdom.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Shaw
authors.affiliation: Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Knogge
authors.affiliation: Institute of Life Science and College of Medicine, Swansea University, Swansea, United Kingdom.
authors.forename: Steven L
authors.initials: SL
authors.lastname: Kelly
authors.affiliation: Institute of Life Science and College of Medicine, Swansea University, Swansea, United Kingdom.
authors.forename: Diane E
authors.initials: DE
authors.lastname: Kelly
authors.affiliation: Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom bart.fraaije@rothamsted.ac.uk.
authors.forename: Bart A
authors.initials: BA
authors.lastname: Fraaije
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D001393:Azoles / Q000494:pharmacology; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics*; D025141:Drug Resistance, Fungal; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics*; D005659:Fungicides, Industrial / Q000494:pharmacology; D001467:Hordeum / Q000382:microbiology; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D001393:Azoles; D005656:Fungal Proteins; D005659:Fungicides, Industrial; D003577:Cytochrome P-450 Enzyme System
keywords: Rhynchosporium; fungicides; gene duplication; resistance; standing variation; triazoles
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