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. 2021 Aug 30;53(9):1373–1384. doi: 10.1038/s41588-021-00914-y

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© The Author(s) 2021

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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Extended Data Fig. 1 — (a) Size distribution of the 30 largest scaffolds in the AmiCal1 assembly. Aca scaf1 to Aca scaf23 match the number of chromosomes in the bowfin genome^21,29 and are thus considered pseudochromosomes. Locations of the four bowfin Hox gene clusters Hox A-D are indicated by colored circles. (b) Hi-C contact map for the 23 pseudochromosomes, generated from blood sample. Resolution: 500-kb bins. The red dashed box indicates Aca scaf15. (c) Hi-C contact map for Aca scaf15. Resolution: 50-kb bins. (d) Topologically Associating Domains (TADs) called using a resolution of 300-kb bin size in the region of Aca scaf15 indicated by the white dashed box in (c). (e) ATAC-Seq profile through bowfin development within the central TAD in (d). ATAC-Seq peaks and ncOCRs are observed for a putative bowfin ortholog of the MCS-R2 hb enhancer in intron 5 of the nprl3 gene known to regulate flanking hemoglobin genes⁶² (red). (f) Conserved synteny of the region containing hemoglobin genes (red highlighted arrows) on bowfin Aca scaf15 to gar, teleosts, and tetrapods, centered on the nprl3 gene (central green arrow) that contains the putative MCS-R2 intronic hb enhancer.

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