Genome-structural analyses support an allotetraploid origin of the walnut family from within Myricaceae and shared genome duplications reveal substitution rate variation

In lineages of allopolyploid origin, entire parental subgenomes may coexist, with two or more sets of homoeologous chromosomes that differ in gene content and syntenic structure. Presence or absence of genes, and microsynteny along chromosomal blocks, can be used to differentiate subgenomes and can be coded as phylogenetic data. We assembled chromosome-level genomes of representative species across an ancient allopolyploid lineage, the walnut family (Juglandaceae), with Myrica and other Fagales as outgroups, and used genome-structural data to infer a phylogeny. Microsynteny (with various collinear block sizes) and gene content analyses, using the dominant or recessive progenitor subgenomes or both, all yielded identical topologies that place Engelhardia (a SE Asian and Central American clade) with Platycarya, an enigmatic monospecific taxon endemic in East Asia, but well-represented in the Paleocene-Eocene of North America and Europe. Morphological studies including fossils also found t...