Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

24 Recent phylogenomic analyses have solved evolutionary relationships between most of the 25 Orchidaceae subfamilies and tribes, yet phylogenetic relationships remain unclear within the 26 42 43 45 46 47 100, PP = 0.77-1.0), and only a few positions remained unresolved. Here, the relationship between 128 Codonorchidae+Orchideae was moderately supported (LBS = 86) together with that of 129 Cymbidiinae and the remaining Cymbidieae (LBS = 62). The monophyly of Nervilieae and 130 Triphoreae was moderately supported (LBS = 79), as well as the phylogenetic relationships of 131 Nervilieae+Triphoreae and the remainder of Epidendroideae (LBS = 75), and Epidendreae and 132 Coelia + Eria (LBS = 52) (Fig. 2). 133 134 2.3 Molecular characterisation of plastid genomes 135 Whole plastome sequences belonging to 97 species (11 sequenced here and 86 reported in 136 NCBI) were annotated for 75 protein-coding genes. Five additional genes were recovered when 137 concatenating this data matrix with the protein coding regions matrix used by Givnish 2 , giving a 138 6

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