Fig. 1

Heatmap showing percent covered by synteny alignment for each 1 Mb window in 15 de novo M. truncatula assemblies (Upper 15 tracks), 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). Nucleotide diversity (θπ) estimates were calculated using only 13 “ingroup” M. truncatula accessions