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. 2020 Apr 3;21:279. doi: 10.1186/s12864-020-6683-0

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© The Author(s). 2020

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.

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Fig. 1 — Manual gene model curation examples. Several tracks are shown: updated gene model (beige background), original (2005) gene annotation (grey background), RNAseq data (white background), transcript assembly (dark green, on green background), and EVM predictions (orange, on green background). a A new gene discovered on the basis of RNAseq data (TpMuguga_03g02005). b A case where two genes in the 2005 annotation merge in the new annotation on the basis of RNAseq read coverage (TpMuguga_04g02435). c A case where a gene in the 2005 annotation has been split into two genes in the new annotation (TpMuguga_04g02190 and TpMuguga_04g02185). d A case where a gene has been reversed in orientation on the basis of RNAseq data (TpMuguga_02g02095). e A case where overlapping genes led to ambiguity in UTR coordinates, and so the UTRs were not defined in this intergenic region (TpMuguga_01g00527 and TpMuguga_01g00528). f A case of a single gene where alternative splicing exists (as seen by significant read coverage in at least one intronic region), but there is one most prevalent isoform (TpMuguga_03g00622). g A case of two genes that overlap by coding sequences. Coding exons are colored by reading frame (TpMuguga_05g00017 and TpMuguga_05g00018)