Fig. 1: Comparative analysis of four de novo pecan genomes.

a A map of syntenic orthologous (transparent blue) and homeologous blocks (gray with black borders) among the four reference genomes and the walnut outgroup. Chromosomes are represented by white segments and are scaled to the same physical size (Mb: megabases) for all genomes. Orthologous chromosomes are stacked vertically and labeled accordingly. b Comparisons of the degree of synteny between homeologous chromosomes across the ‘Pawnee’, walnut, maize, and poplar genomes. The dotplots display the gene-rank-order positions of syntenic blastp hits along the main genome (x axis) and homoeologous chromosomes (y axis). Chromosomal bounds are shaded by the total number of blast hits found between each pair of homeologous chromosomes. c Across the pan-genome, the vast majority of all genes are found in orthogroups that contain all four pecan genomes (bars shaded black); however, genes private to each genome (shaded orange) and, to a lesser degree, shared among >1 genome (gray) are also common. Filled circles represent presences in orthogroups; open circles are absences. d The high level of synteny between the pecan genomes and walnut allowed for simple pan-genome construction and gene ordering. Here, each point represents the location of a gene by its rank-order location within each de novo genome assembly (x axis) and the inferred syntenic position in the pan-genome (y axis). Source data are provided as a Source Data file.