Fig. 1. Structure and phylogeny of Juglans genomes.

a Circular plot of the Juglans regia pseudomolecules. Circles from outside to inside are: pseudomolecule coordinates in Mb, density of all types of LTR-RTs, density of Gypsy LTR-RTs, density of Copia LTR-RTs, and gene density. Central lines connect syntenic blocks across chromosomes. Different colors represent different homoeologous chromosome pairs derived from the Juglandoid WGD. b Dot-plot alignments of the JrSerr_v1.0 pseudomolecules against Jm31.01_v1.0 pseudomolecules. The starts of the pseudomolecules are to the left or bottom. The blue diagonal across the plots of the 16 chromosomes indicate collinearity of homoeologous chromosomes between the two genomes. The green dots indicate homoeologous chromosomes within a genome, which originated by the Juglandoid WGD. The short black and red dot traces indicate paralogues produced the γ whole genome triplication