Deciphering Genome Content and Evolutionary Relationships of Isolates from the FungusMagnaporthe oryzaeAttacking Different Host Plants

Abstract

Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).

Molecular mechanisms regulating plant infection in the rice blast fungus Magnaporthe oryzae

“…This suggests that transposition events might play an important role in genome variation in the rice blast fungus, which can explain the rapid adaptation of M. oryzae isolates to new resistant rice varieties (Zeigler, 1998, Kang, et al, 2001. This has been confirmed by additional whole genome comparative studies which have increased our understanding on the genetic mechanisms that drive host specialization in Magnaporthe species (Chiapello, et al, 2015, Yoshida, et al, 2016, Zhong, et al, 2016. Gene gain or loss and chromosomal rearrangements facilitated by transposable elements seem to be the main mechanism that drives host adaptability during Magnaporthe species coevolution processes (Yoshida, et al, 2016, Zhong, et al, 2016.…”

“…Transposable elements are important determinants of fungal genome evolution since they are drivers of macro-micro rearrangements, inducers of point mutations in surrounding coding or noncoding regions, and modifiers of gene expression (Beare, et al, 2009, Rouxel, et al, 2011, Grandaubert, et al, 2014, Chiapello, et al, 2015, Ai, et al, 2016, Yoshida, et al, 2016. The control of their expression is crucial for the correct function of the cell.…”

“…Gene gain or loss and chromosomal rearrangements facilitated by transposable elements seem to be the main mechanism that drives host adaptability during Magnaporthe species coevolution processes (Yoshida, et al, 2016, Zhong, et al, 2016. Whole genome sequencing studies have also confirmed that there is a strong conservation of genome composition among M. oryzae field isolates, and this include specific gene families encoding effectors and secondary metabolites that can regulate host specificity in M. oryzae (Chiapello, et al, 2015).…”

“…The second lineage contains rice and related fungal isolates from Triticum, Avena and Setaria and has been renamed as a new species, M. oryzae, although no morphological differences exist between isolates of these two groups. Whole genome sequencing approaches have corroborated this lineage (Chiapello, et al, 2015). There is an important debate about the maintenance of the genus Chapter 1: Introduction Magnaporthe or Pyricularia for the rice blast fungus among community members (http://www.magnaporthe.blogspot.com.es/).…”

Plant pathogenic Magnaporthales in Australia, with particular reference to Pyricularia oryzae on wild and cultivated rice

“…Whole genome studies of fungal pathogens can be used to better understand many aspects of biology including climate adaptation and host range shift, as well as to monitor the breakdown of plant disease resistance or the emergence of fungicide resistance (Chiapello et al, 2015). To date, 53 isolates of Pyricularia oryzae have been sequenced and published (http://www.ncbi.nlm.nih.gov), which is a reflection of the importance of this species, however there are no genomes sequenced from Australian isolates.…”