Assembly and annotation of eleven Salix (shrub willow) genomes

The shrub willows (Salix section Vetrix) are an emerging bioenergy crop in
North America and Eurasia. However, genomics resources in this section are
still quite limited, with only a few reference genomes available, despite
many species in use in breeding programs. Here we present de novo
assemblies and annotations of eleven shrub willow genomes from six
species. Copy number variation of candidate sex determination genes within
each genome was characterized and revealed remarkable differences in
putative master regulator gene duplication and deletion. We also analyzed
copy number and expression of candidate genes involved in floral secondary
metabolism and identified substantial variation across genotypes, which
can be used for parental selection in breeding programs. Lastly, we report
on a genotype that produces only female descendants and identified gene
presence/absence variation in the mitochondrial genome that may be
responsible for this unusual inheritance.