A new reference genome shows the one-speed genome structure of the barley pathogen ramularia collo-cygni

Remco Stam, Martin Münsterkötter, Saurabh Dilip Pophaly, Like Fokkens, Hind Sghyer, Ulrich Güldener, Ralph Hückelhoven, Michael Hess

Research output: Contribution to journalArticlepeer-review

24 Scopus citations

Abstract

Ramularia leaf spot has recently emerged as a major threat to barley production world-wide, causing 25% yield loss in many barley growing regions. Here, we provide a new reference genome of the causal agent, the Dothideomycete Ramularia collo-cygni. The assembly of 32 Mb consists of 78 scaffolds. We used RNA-seq to identify 11,622 genes of which 1,303 and 282 are coding for predicted secreted proteins and putative effectors respectively. The pathogen separated from its nearest sequenced relative, Zymoseptoria tritici 27 Ma. We calculated the divergence of the two species on protein level and see remarkably high synonymous and nonsynonymous divergence. Unlike in many other plant pathogens, the comparisons of transposable elements and gene distributions, show a very homogeneous genome for R. collo-cygni. We see no evidence for higher selective pressure on putative effectors or other secreted proteins and repetitive sequences are spread evenly across the scaffolds. These findings could be associated to the predominantly endophytic life-style of the pathogen. We hypothesize that R. collo-cygni only recently became pathogenic and that therefore its genome does not yet show the typical pathogen characteristics. Because of its high scaffold length and improved CDS annotations, our new reference sequence provides a valuable resource for the community for future comparative genomics and population genetics studies.

Original languageEnglish
Pages (from-to)3243-3249
Number of pages7
JournalGenome Biology and Evolution
Volume10
Issue number12
DOIs
StatePublished - 1 Dec 2018

Keywords

  • Barley pathogen
  • Dothideomycetes
  • Fungi
  • Genome
  • Phytopathology

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