The Soursop Genome (Annona muricata L., Annonaceae)

Abstract

The Annonaceae family contains important tropical crops, but the number of species used commercially is limited, and development of other promising species for cultivation is hindered by a lack of genomic resources to support the building of breeding programmes. The family is part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide novel resources to both plant breeders and evolutionary research, we described the chromosome-level genome assembly of the soursop (Annona muricata L.), using DNA data generated with PacBio and Illumina short-read technology, in combination with 10XGenomics, BioNano data, and Hi-C sequencing. To disentangle key angiosperm relationships, we reconstructed phylogenomic trees comparing a wider sampling of available angiosperm genomes and reveal that the soursop represents a genomic mosaic supporting different evolutionary histories, with scaffolds almost exclusively supporting singular topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previously published whole genome-based studies remained inconclusive. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history. The soursop is the first genome assembled in Annonaceae and supports further studies of floral evolution in magnoliids, whilst providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement in promising Annonaceae fruit crops and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource will further strengthen the role of Annonaceae as a model group for research on the ecology, evolution, and domestication potential of tropical species in pomology and agroforestry.