Fig. 1: Syntenic characterization of the TM-1 and Hai7124 genomes.

a, Collinearity on chromosome A01 for the TM-1 (v1.1) and TM-1 (v2.1) genomes. The red region in the blue bar indicates the centromeric region identified by alignment of CRGs. Gray lines indicate collinearity between the two genomes; each line represents a unique mapping alignment >5 kb in length. Yellow bars show the CenH3-binding regions in each genome; adjusted ChIP-seq reads were calculated for a 100-kb sliding window at 10-kb intervals. GC content, repeat distribution and gene density in a 1-Mb sliding window are shown at 100-kb intervals. A comparison of TM-1 Bionano optical maps (blue) and the TM-1 (v2.1) genome (green) is shown. Right, TM-1 Hi-C contact data mapped onto the TM-1 (v2.1) genome. The heat map represents the normalized contact matrix. b, Collinearity on chromosome A01 for the Hai7124 (v1.1) and 3-79 genomes. Data are presented as in a. c, Analysis of the synteny among multiple Gossypium genomes. Macrosynteny connecting blocks of >30 one-to-one gene pairs is shown. Blue links indicate translocation between the D subgenome of allotetraploid cotton and the D genome of diploid cotton; yellow links indicate translocation between the A genome and the D genome in diploid cotton; and green links indicate translocation between the A subgenome of allotetraploid cotton and the A genome of diploid cotton. d, MCScanX was performed to identify the collinearity between genes in the TM-1 (v2.1) and Hai7124 (v1.1) genomes. Each block includes >30 gene pairs.