Extended Data Fig. 4: Deeply diverged pericentromic haplotypes on chromosome 5H.
From: A haplotype-based evolutionary history of barley domestication
(a) Sequence divergence (SNPs per Mb) on chromosome 5H between wild barleys WBDC260 (SL) and WBDC208 (CA). (b) Neighbor-joining tree of wild and domesticated barleys including 48 samples from the pangenome of Jayakodi et al.16 based on the SNPs between 150–230 Mb on chr5H. (c) Collection sites of wild barleys carrying either haplotype. The “green” haplotype is most common in the SL population. Geographical outlines were obtained from the R package ‘maps’ (https://CRAN.R-project.org/package=maps), which uses public domain base map data (under a GNU General public license: version 2). (d) Frequencies of both haplotypes in wild and domesticated barley populations. (e) Alignments on chromosome 5H, 100 to 300 Mb between sequence assemblies of wild (w) and domesticated (d) pangenome accession with either haplotype to the MorexV3 reference. The accession names are indicated on the y-axis. In panels (a) and (e), the boundaries of divergent haplotypes (150 to 230 Mb) are marked by blue shading and the dashed line at 205 Mb indicates the position of the centromere in the MorexV3 reference.
