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. 2021 Apr 28;592(7856):737–746. doi: 10.1038/s41586-021-03451-0

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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, b, Steps and NG50 continuity values of the VGP assembly pipeline that gave the highest quality assembly for Anna’s hummingbird (a) and Canada lynx (b) in this study. The specific steps are outlined further in Extended Data Fig. 2a, and Methods. c, Whole-genome alignment of CLR (red), linked reads (green), optical maps (blue), and Hi-C reads (purple) of the Anna’s hummingbird, along with telomere motif (TTAGGG and its reverse complement, yellow) and gaps (grey) using Asset software¹⁰³. For each data type, the first row shows the mapped coverage, and the second shows the number of counts of low coverage or signs of collapsed repeats. Larger chromosomal scaffolds (1–19) have fewer gaps and low coverage or collapsed regions compared with the micro chromosomes (20–33). Chromosomes 14, 15 and 19 of the Anna’s hummingbird were the most structurally reliable scaffolds, having only one gap each with no low-support regions. We defined reliable blocks as those supported by at least two technologies. Reliable blocks excluded regions with structural assembly errors, such as collapsed repeats or unresolved segmental duplications. Low-support regions are those where the reliable blocks row has a peak.