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A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni
Tech Univ Munich, Sch Life Sci Weihenstephan, Chair Phytopathol, Munich, Germany.ORCID iD: 0000-0002-3444-6954
Univ Sopron, Res Ctr Forestry & Wood Ind, Funct Genom & Bioinformat, Sopron, Hungary;Helmholtz Ctr Munich, Inst Bioinformat & Syst Biol, Neuherberg, Germany.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Tech Univ Munich, Sch Life Sci Weihenstephan, Sect Populat Genet, Munich, Germany;Ludwig Maximilians Univ Munchen, Fac Biol 2, Div Evolutionary Biol, Munich, Germany.
Univ Amsterdam, Swammerdam Inst Life Sci, Mol Plant Pathol, Amsterdam, Netherlands.
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2018 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 10, no 12, p. 3243-3249Article in journal (Refereed) Published
Abstract [en]

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 similar to 27Ma. 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.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2018. Vol. 10, no 12, p. 3243-3249
Keywords [en]
fungi, phytopathology, genome, dothideomycetes, barley pathogen
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-375575DOI: 10.1093/gbe/evy240ISI: 000455327200011PubMedID: 30371775OAI: oai:DiVA.org:uu-375575DiVA, id: diva2:1284503
Funder
German Research Foundation (DFG)Available from: 2019-01-31 Created: 2019-01-31 Last updated: 2019-01-31Bibliographically approved

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