A large accessory genome and high recombination rates may influence global distribution and broad host range of the fungal plant pathogen Claviceps purpurea

PLoS One. 2022 Feb 10;17(2):e0263496. doi: 10.1371/journal.pone.0263496. eCollection 2022.

Abstract

Pangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (~ 38%), high recombination rates (ρ = 0.044), and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion may be controlled by frequent recombination. We additionally identified that within the ergoline biosynthetic cluster the lpsA1 and lpsA2 were the result of a recombination event. However, the high recombination rates observed in C. purpurea may be influencing an overall trend of purifying selection across the genome. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Claviceps / genetics*
  • DNA Transposable Elements
  • Genome, Fungal*
  • Host Specificity
  • Polymorphism, Single Nucleotide
  • Recombination, Genetic*
  • Selection, Genetic

Substances

  • DNA Transposable Elements

Grants and funding

This work was supported by the Agriculture and Food Research Initiative (AFRI) National Institute of Food and Agriculture (NIFA) Fellowships Grant Program: Predoctoral Fellowships grant no. 2019-67011-29502/project accession no. 1019134 from the United States Department of Agriculture (USDA), the American Malting Barley Association grant no. 17037621, and the U.S. Department of Agriculture, Agricultural Research Service. Dr. Broders was supported in part by the Simon’s Foundation Grant number 429440 to the Smithsonian Tropical Research Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.