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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.

plos one

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