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

PLoS One. 2015 Nov 11;10(11):e0142215. doi: 10.1371/journal.pone.0142215. eCollection 2015.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Plant / chemistry
  • DNA, Plant / genetics
  • Evolution, Molecular
  • Gene Dosage
  • Genome, Chloroplast / genetics*
  • Inverted Repeat Sequences / genetics*
  • Molecular Sequence Data
  • Multigene Family
  • Mutation*
  • NADH Dehydrogenase / genetics*
  • Orchidaceae / classification
  • Orchidaceae / genetics*
  • Phylogeny
  • Plant Proteins / genetics*
  • Pseudogenes / genetics
  • Sequence Analysis, DNA
  • Species Specificity


  • DNA, Plant
  • Plant Proteins
  • NdhF protein, plant
  • NADH Dehydrogenase

Associated data

  • GENBANK/KM032623
  • GENBANK/KM032624
  • GENBANK/KM032625
  • GENBANK/KP205432
  • GENBANK/KR260986
  • GENBANK/KT388108
  • GENBANK/KT388109

Grants and funding

This work was supported by a grant from the American Orchid Society ( and grants MEST 2012-044048 and MEST 2010-0029131 from the National Research Foundation of Korea ( The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.