Epidendroideae

Abstract: Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.

Abstract: Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.

Abstract: Phylogenetic relationships within the epidendroid orchids with emphasis on tribes Epidendreae and Arethuseae were assessed with parsimony and model-based analyses of individual and combined DNA sequence data from ITS nuclear ribosomal DNA and plastid trnL intron, the trnL-F spacer, matK (gene and spacers), and rbcL regions. Despite the absence of boostrap support for some of the relationships, a well-resolved and supported consensus was found, for which most clades were present in more than one individual analysis. Most clades of this consensus attained high posterior probabilities with a Bayesian approach. Circumscription of Arethuseae and Epidendreae are different from most orchid systems based on morphology, but they correspond to a combination of patterns from several less comprehensive orchid phylogenetic analyses previously published. A new circumscription of Epidendreae includes only Neotropical subtribes (Bletiinae, Chysiinae, Laeliinae, Ponerinae, and Pleurothallidinae), whereas Arethuseae include Coelogyninae (all Old World) and Arethusinae (pantropical). Many previously included genera will need to be moved to other tribes. Taxa previously assigned to be Old World Epidendreae are related to different groups of Old World orchids, and this study can serve as a guide for sampling strategies in future studies to resolve troublesome epidendroid orchid clades.