@ARTICLE{TreeBASE2Ref29629, author = {yunxia li and Xiao-Hua Jin}, title = {Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.}, year = {2019}, keywords = {Cypripedioideae, mitochondrial genome, mycoheterotrophic orchids, Orchidaceae, plastid genome, Vanilloideae}, doi = {10.1016/j.ympev.2019.106540}, url = {http://}, pmid = {}, journal = {Molecular Phylogenetics and Evolution}, volume = {139}, number = {}, pages = {106540}, abstract = {To advance our knowledge of orchid relationships and timing of their relative divergences, we used 76 protein-coding genes from plastomes (ptCDS) and 38 protein-coding genes from mitochondrial genomes (mtCDS) of 74 orchids representing the five subfamilies and 18 tribes of Orchidaceae, to reconstruct the phylogeny and temporal evolution of the Orchidaceae. Our results indicated the backbone of Orchidaceae is well supported with both datasets, but there are conflicts between these trees. The phylogenetic positions of two subfamilies (Vanilloideae and Cypripedioideae) are reversed in these two analyses. The phylogenetic positions of several tribes and subtribes, such as Epipogiinae, Gastrodieae, Nerviliinae, and Tropidieae, are well resolved in mtCDS tree. Thaieae have a different position among higher Epidendroideae, instead of sister to the higher Epidendroideae. Interrelationships of several recently radiated tribes within Epidendroideae, including Vandeae, Collabieae, Cymbidieae, Epidendreae, Podochileae, and Vandeae, were resolved with good support in the ptCDS tree, but most are not in the mtCDS tree. Conflicts between the two datasets may be attributed to the different substitution rates in these two genomes and heterogeneity of substitution rate of plastome. Molecular dating indicated that the first three subfamilies, Apostasioideae, Cypripedioideae and Vanilloideae, diverged relatively quickly, and then there was a longer period before the last two subfamilies, Orchidoideae and Epidendroideae, began to radiate. Most mycoheterotrophic clades of Orchidaceae evolved in the last 30 million years with the exception of Gastrodieae. } }

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