Phylogenomics and Floristic Origin of Endiandra R.Br (Lauraceae) from New Caledonia

New Caledonia is a biodiversity hotspot with flora closely related to that of Australia and has received considerable attention. Endiandra (Cryptocaryeae: Lauraceae) is distributed from tropical Asia to Oceania, including New Caledonia, with northeastern Australia and New Guinea as diversity centers, but the genus in New Caledonia remains understudied. Here, four species of Endiandra native to New Caledonia were sequenced, and their complete plastome sequences were analyzed. A plastome-based phylogenomic tree of Cryptocaryeae was reconstructed, and divergence times were estimated. The phylogenomic tree supports the monophyly of Endiandra. Interestingly, the species of Endiandra from New Caledonia were grouped into two separate subclades, with one subclade including three species and the other subclade containing only one species. The stem and crown ages of the first subclade were 33.18 Ma and 14.5 Ma, respectively, and the second subclade diverged by approximately 10.36 Ma. The structural characteristics of the newly sequenced plastomes were compared with those of Beilschmiedia species from different continents. The results indicate that the plastome sequences of the four species of Endiandra are longer than those of Beilschmiedia. Additionally, Endiandra has more simple sequence repeats (SSRs) than Beilschmiedia, though the difference is slight. The Guanine-Cytosine (GC) content of Endiandra was lower than that of Beilschmiedia. Five highly variable regions were identified, including matK-rps16, ycf1, petA-psbJ, petN-psbM, and ndhF. The Endiandra species in New Caledonia originated through long-distance dispersal followed by local divergence, rather than vicariance. Additionally, we identified at least two instances of floristic exchange between New Caledonia and Australia. Our study provides further evidence for understanding the biogeographic history between these two regions.