Phylogenetic relationships among Australian native citrus species based upon complete chloroplast genomes and single copy nuclear genes

Citrus is widely consumed across the world as a fruit crop. Despite many citrus species being extensively studied around the world, phylogenetic relationships among Australian native species remain unresolved. Here we present the phylogenetic relationships among six Australian native species, two domesticated citrus cultivars of commercial importance in Australia, and another 13 accessions cultivated internationally based on complete, de novo assembled chloroplast genomes and 86 single copy nuclear genes. The chloroplast and nuclear phylogenies were topologically different. The Australian species formed a monophyletic clade based on their nuclear genes. The nuclear phylogeny revealed a close relationship between Citrus inodora and Citrus australasica. These two species were distinct from the other four Australian limes that were more closely related to each other. Citrus australasica had a unique chloroplast which was distinct from all other Australian limes. Among the other Australian limes, Citrus glauca was the most distinct species based on nuclear genes, however, it had a similar chloroplast sequence to C. australis. The undetermined Citrus sp. was more closely related to Citrus garrawayi, indicating that it is a distinct form of Citrus garrawayi. Citrus medica, had a chloroplast similar to Australian species. However, the nuclear gene phylogeny analysis revealed that C. medica was more closely related to Asian citrus species. This study improves our understanding of phylogenetic relationships among Australian citrus species and confirms their unique status within the genus since it formed a monophyletic clade which was clearly separated from the other non-Australian species.