title: Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries.
abstract: Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.
authors.affiliation: Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea.
authors.forename: Hyoung Tae
authors.initials: HT
authors.lastname: Kim
authors.affiliation: Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea.
authors.forename: Jung Sung
authors.initials: JS
authors.lastname: Kim
authors.affiliation: Department of Biology, Oberlin College, Oberlin, Ohio, United States of America.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Moore
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Kurt M
authors.initials: KM
authors.lastname: Neubig
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Norris H
authors.initials: NH
authors.lastname: Williams
authors.affiliation: Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America.
authors.forename: W Mark
authors.initials: WM
authors.lastname: Whitten
authors.affiliation: Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, Korea.
authors.forename: Joo-Hwan
authors.initials: JH
authors.lastname: Kim
mesh_terms: D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage; D054628:Genome, Chloroplast / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D009154:Mutation; D009245:NADH Dehydrogenase / Q000235:genetics*; D029595:Orchidaceae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; C489904:NdhF protein, plant; D009245:NADH Dehydrogenase