Fig. 1: Geographical distribution and features of Armeniaca species.

a Map of species distribution and of plant material used in this study (Supplementary Data 1). The European and Irano-Caucasian cultivated apricots include 39 modern cultivars from North America, South Africa and New Zealand that are not represented on this map. Orange circles: P. brigantina, pink circles: P. mume, beige circles: P. mandshurica; rectangles: P. armeniaca cultivars and landraces (European in grey, Chinese in purple, Central Asian in blue); red stars: wild Southern Central Asian P. armeniaca (S_Par); yellow stars: wild Northern Central Asian P. armeniaca (N_Par); blue triangles: wild Northern Eastern Chinese P. sibirica (NE_Psib); green triangles: wild Western Chinese P. sibirica (NW_Psib). b Close-up of the Central Asian Prunus armeniaca (Par) natural population. Northern P. armeniaca populations (N_Par) are located over the Zailiysky Mountains while Southern P. armeniaca (S_Par) populations lay over the foothills of the Ferghana valley. c Pictures of the species analysed. d Circos plot showing features of the Marouch #14 Prunus armeniaca genome. Outermost to innermost tracks show the gene density heat map in 250 kb bins (a), transposable element (TE, b) density in 250 kb bins. The red color indicates higher density while the blue color indicates lower density. c–f represent structural variations (insertions in blue, deletions in green, inversions in red, and duplications in purple). For each track from (c)–(f), the outer layer corresponds to P. armeniaca cv. Stella, the middle layer to the P. sibirica CH320.5 and the inner layer to the P. mandshurica CH264.4 line. Maps are licensed as Creative commons for Stamen design. Pictures by S. Liu, S. Decroocq or licensed as Creative commons (P. brigantina flower). The picture of cv. Sefora apricot (P. armeniaca) fruits was kindly provided by CEP INNOVATION. Source data underlying Fig. 1d are provided as a Source Data file and in Supplementary Data 8.