A new avocado reference genome provides insight into genome evolution and the genetic basis of important traits

Long-read sequencing technologies have allowed researchers to characterize genomes with increasing accuracy, leading to a greater understanding of the genetic basis of phenotypes and adaptation. However, many economically important crops lack suitable genomic tools and annotations. This has been the case for the avocado (Persea americana), a perennial crop with high nutritive content. To help address the need for genomic approaches in avocado, we created a reference genome from the Gwen varietal, which is closely related to the agronomically dominant Hass varietal and is a current focus of breeding programs. We produced a 1,032Mb genome assembly with an N50 of 3.37Mb and a BUSCO score of 91%; we also scaffolded the assembly using a genetic map. In addition to producing a scaffolded reference, we resequenced 21 avocados that represented both the three botanical races of P. americana and also three additional closely related outgroup species. Using these data, along with previously published datasets, we: i) characterized the repeat content of the Gwen genome, which constitutes 61% of the genome ii) built a genome annotation with 60,151 genes, which is ~2x more than a previous annotation of the fragmented Hass genome assembly, iii) investigated population structure among our sample of 31 avocados, and iv) performed pairwise comparisons of different groups of avocados to identify genomic regions of high differentiation. The pairwise comparisons included two kinds of contrasts. The first was between botanical races; we reasoned that genomic regions of high differentiation may contain genes that affect the phenotypic traits that differ between races. Using this approach, we identified numerous candidate genes of potential agronomic importance with gene ontology functions that included stress responses, disease resistance, and water osmoregulation. The second contrast was between accessions with differing flowering types that define synchronous dichogamy in avocado. Our analyses of flowering types identified candidate genes hypothesized to affect flower development and circadian rhythms.