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. 2019 Nov 29;10:5468. doi: 10.1038/s41467-019-13427-4

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© The Author(s) 2019

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 — The zebra finch germline-restricted chromosome contains genes copied from many A chromosomes. a, b Cytogenetic evidence for GRC absence in muscle a and GRC presence in the testis b of the same bird (Spain_1) using fluorescence in-situ hybridisation (FISH) of our new GRC-amplified probe dph6 (selected due its high germline/soma coverage ratio; cf. e, f). Note that the single-copy A-chromosomal paralog of dph6 yields no visible FISH signal, unlike the estimated 308 dph6 copies on the GRC. The scale bar indicates 10 μm. c, d Comparison of germline/soma coverage ratios for 1 kb windows with an expected symmetrical distribution (blue bars) indicates enrichment of A-chromosomal single-copy regions in the germline (red bars), similar to lamprey², both in Seewiesen (c; linked reads) and Spain (d; average of Spain_1 and Spain_2 coverage; PCR-free short reads) samples. Y-axis is truncated for visualisation. e, f Manhattan plot of germline/soma coverage ratios in 1 kb windows across chromosomes of the somatic reference genome taeGut2. Colours indicate high-confidence GRC-linked genes and their identification (red: coverage, blue: SNVs, purple: both; Supplementary Table 5). Note that the similarities between Seewiesen e and Spain_1/Spain_2 averages f constitute independent biological replicates for GRC-amplified regions, as the data are based on different domesticated populations and different library preparation methods. Red arrows denote two FISH-verified GRC-amplified regions (cf. b)⁸. Only chromosomes >5 Mb are shown for clarity. g, h Linked-read barcode interaction heatmaps of an inter-chromosomal rearrangement on the GRC absent in Seewiesen liver g but present in Seewiesen testis h. i, j Coverage plots of two examples of GRC-linked genes that are divergent from their A-chromosomal paralog, trim71 i and napa j¹⁰, and thus have very low coverage (normalised by total reads and genome size) in soma.