Recent progress on genome assemblies and annotation of six pistachio cultivars

Plant breeding has been revolutionized by the advent of high-throughput genome sequencing, which provides valuable insights into the genetic basis of crops and enables the development of novel and improved cultivars. This is particularly important for long-lived crops such as pistachio since the breeding cycle is much longer than annual crops. To facilitate genome-enabled breeding efforts for improved pistachio cultivars, especially in the face of emerging environmental stresses, an international collaboration spanning five institutes and countries is working to create a pistachio pan-genome. We recently sequenced the genomes of six diverse pistachio genotypes with PacBio HiFi sequencing. Gene discovery (annotation) was facilitated by whole transcriptome data from multiple tissues with Iso-Seq in each genotype. These data provide an early glimpse into functional genomic diversity in pistachio and the basis to begin discovering targets for accelerated breeding. We discuss progress and promise to further develop and apply these new genomic resources.