Fig. 2

Zoom-in view of five 1-Mb regions (a-e) selected from Fig. 1. Upper 15 tracks show percentage covered by synteny alignment for each 50 kb window (column) in 15 M. truncatula assemblies. Bottom tracks show reference gap position (‘Gaps’), percent bases covered by synteny blocks in at least 10 out 13 accessions (‘Coverage’), nucleotide diversity (θπ) for SNPs (‘Pi_SNP’), short InDels (<50 bp, ‘Pi_InDel’) and large SVs (> = 50 bp, ‘Pi_SV’), as well as gene density of different categories (TE, NBS-LRR, RLK, NCR, LRR and F-boxes) in relative scale (minimum to maximum spaced equally in grayscale within each panel) with grey columns representing missing data due to lack of synteny coverage. Starting poisition for each region is provided at the bottom (e.g., chr7:28 Mb, indicating that a 1 Mb region beginning at position 28,000,001 on chromosome 7 is displayed)