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. 2017 Aug 22;7:9042. doi: 10.1038/s41598-017-07995-y

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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The SMRT genome assembly of Forc016 includes eleven core chromosomes, several repeat-rich, gene-poor accessory regions and one chromosome enriched in candidate effector genes. Comparison of the Forc016 assembly to that of Fol4287 reveals (A) eleven conserved core chromosomes (light blue), one putative pathogenicity chromosome (red) and several other accessory sequences (dark blue). Accessory regions typically have (B) low gene density and (C) high repeat density, both calculated here in 50 kb windows. The putative pathogenicity chromosome is marked by (D) the presence of many candidate effector genes. (E) Indicates nucmer alignments with the Fol4287 reference assembly: in red alignments to the putative pathogenicity chromosome of Forc016, in dark blue alignments from known accessory regions in Fol4287 (chr1B; chr2B; chr3; chr6; chr14; chr15) and in light blue the remaining alignments, mostly between core regions in both genomes.