Fig. 1

Schematic diagram for reassembling of G. arboreum chromosome 12 (A_A12). Each rectangle corresponded to procedures applied for chromosome reassembling steps. Genotypic data of 24,569 SNP markers used in previous study [27] was first filtered out for construction of linkage groups, which were then assigned to 13 chromosomes of G. arboreum. Afterwards, linkage group belong to G. arboreum chromosome 12 was used for re-assembling. We checked the alignments of scaffolds belonging to G. arboreum chromosome 12 for following levels: (i) Alignment of G. arboreum scaffolds (obtained by the genetic map) to G. raimondii scaffolds [7], (ii) Orientation of G. raimondii (obtained from the previous step) and G. arboreum scaffolds along G. raimondii chromosome (D_D08) [36], and (iii) adjacency of G. arboreum scaffolds within G. hirsutum chromosome (AD_A12) [8]