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In total, 31 incorrectly joined genes and 52 incorrectly split genes could be identified.
A gene containing 18 exons was incorrectly split by both tools (GRMZM2G119544_E01 and GRMZM2G119496_E01).
Incorrectly split or joined genes: This category refers to adjacent genes that were incorrectly joined in the annotation of the Broad Institute or individual genes that were incorrectly split due to misinterpretation of the genomic sequence data.
Comparing the 10 component linkage maps with each other allowed us to identify and correct inconsistencies, including incorrectly split or joined LGs.
Vice versa, incorrectly split genes could be found by a largely uniform read coverage throughout the sequence of the incorrectly annotated gene.
A website showing all gene clusters are included as Additional file 1. Gene cluster diagrams also include domain annotations, but these are not manually curated and some domains are incorrectly split in half.
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These modifiers should be retained whereas in some wrong cases (e.g. 'Fluorophenyl substituted 3,3'-diindolylmethane') the mention was incorrectly splitted.
For example, Mugsy sometimes failed to align local regions that had repetitive sequences, thus incorrectly splitting some chemotype-specific alignments.
Our data indicate that up to 11% of the genes in the v1 annotation are split incorrectly, similar to the error rate in other annotated plant genomes [ 43].
We also detected 462 of these genes and our analysis suggested that 75% of them were split incorrectly in the v1 annotation.
However, Donohue's letter may be incorrectly addressed, as Time Warner Cable split off from Time Warner HBOO's parent company) in 2009.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com