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. 2018 May 22;19:381. doi: 10.1186/s12864-018-4750-6

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© The Author(s). 2018

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — Identification of orthologous gene groups and gene pairs between the Bgh isolates DH14 and RACE1. a Bar graph visualizing the number of gene models in DH14 and RACE1 that were assigned by OrthoFinder into single copy orthogroups (with one member per isolate), orthogroups with more than two members, or with no ortholog at all. b Bar graph summarizing the observed orthology relationships between DH14 and RACE1 gene models, as inferred from a combination of OrthoFinder results and additional manual inspection of gene positions and synteny. With this method, a one-to-one relationship between isolates could be established for most genes (6844), while for ~ 200 genes in each isolate the relationship remained ambiguous (e.g. due to the existence of additional identical copies). Through further integration of RNA-seq data for both isolates, 31 and 27 genes were verified to be isolate-specific in DH14 and RACE1, respectively. For the remaining genes (47 in DH14 and 162 in RACE1) the relationship assignment was inconclusive due to still existing inaccuracies in the assemblies or annotations. c Graphical representation showing the composition of the identified orthologous gene groups from the OrthoFinder analysis. Most groups (6200 out of 6319) contain an equal number of members in DH14 and RACE1 (gray squares), while for some an isolate-specific enlargement can be observed with more members in one isolate than the other (light blue and pink squares)