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. 2020 Jul 24;7:249. doi: 10.1038/s41597-020-00581-4

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© The Author(s) 2020

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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Fig. 1 — Merging DM Phureja PGSC and ITAG gene models. (a) Decision tree for the merging of both genome models, with 6 possible outcomes: singleton genes (‘keep gene as is’), manual curation (‘gene cluster to manual curation’ and programmatic solution (all remaining 4 options). Green solid lines represent a satisfied condition (Y: Yes), dashed red lines, an unsatisfied condition (N: No). (b) Example of manual curation in the merged DM genome GTF, region visualisation (chr12:11405699..11418575) in the Spud DB (solanaceae.plantbiology.msu.edu) Genome Browser¹³. ITAG defined Sotub12g014200.1.1 spans three PGSC defined coding sequences (PGSC0003DMT400005728, PGSC0003DMT400005745 and PGSC0003DMT400005726). Below the gene models, RNA sequence tracks are shown, showing how these genes are expressed in various plant organs. In the concrete case, Sotub12g014200.1.1 was preferred due to RNA-Seq evidence being in concordance, and no evidence for PGSC0003DMT400005745.