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. 2020 Aug 10;21:202. doi: 10.1186/s13059-020-02074-4

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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. 4 — Structure of the ancestral chromosome 16p13 locus. The structure and organization of chr16p13 in four primate lineages is shown based on sequencing of a tiling path of BAC clones for each primate haplotype. SDs (colored arrows) and gene models (black arrows) are shown with respect to lineage-specific duplications (blue bars) identified based on sequence read-depth (WSSD) [1]. a The chromosome 16p13 region has expanded and contracted hundreds of kilobases due to lineage-specific duplication. Note the ancestral ~ 160-kbp inversion between the human RP11 haplotype and all other primates. The ancestral LCR16a duplicon in macaque shows a single copy of NPIP, compared to three copies in marmoset and chimpanzee, and five copies in human. b A Miropeats comparison between two human haplotypes at the ancestral locus on chr16p13. CHM1 BACs tiling across the chr16p13 region were sequenced and assembled using PacBio SMRT sequencing to create a super contig. The SD organization is depicted using colored arrows. Miropeats between RP11 and CHM1 contigs shows pairwise differences between orthologous regions. A ~ 400-kbp inversion is detected in the CHM1 haplotype, flanked by LCR16a core duplicons (blue lines). CHM1 also carries an additional duplication corresponding to LCR16a-009, which contains PDXDC1 (maroon arrow) and incomplete duplication of LCR16a-021 NOMO1 (blue arrow)