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. 2019 Nov 7;10:5068. doi: 10.1038/s41467-019-12927-7

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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 — Strategy to identify homologous contigs in genome assemblies by gene synteny. To detect shared content, Pgt gene models²¹ (grey and coloured boxes) were aligned to the genome assemblies and the contig positions of the top two hits of each gene were recorded. Contigs containing at least five shared genes were considered as potential haplotype pairs. Sequence collinearity between contigs was assessed by alignment, and homologous matching contigs were assigned to bins. Examples shown are for Bin04 and Bin12 from Pgt21-0 and Ug99, respectively