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Background   Oncidium  spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic identification very difficult. Molecular markers derived from the chloroplast genome can provide useful tools for phylogenetic resolution.    Results  The complete chloroplast genome of the economically important  Oncidium  variety  Onc . Gower Ramsey (Accession no. GQ324949) was determined using a polymerase chain reaction (PCR) and Sanger based ABI sequencing. The length of the  Oncidium  chloroplast genome is 146,484 bp. Genome structure, gene order and orientation are similar to  Phalaenopsis , but differ from typical Poaceae, other monocots for which there are several published chloroplast (cp) genome. The  Onc . Gower Ramsey chloroplast-encoded  NADH dehydrogenase  ( ndh ) genes, except  ndhE , lack apparent functions. Deletion and other types of mutations were also found in the  ndh  genes of 15 other economically important Oncidiinae varieties, except  ndhE  in some species. The positions of some species in the evolution and taxonomy of Oncidiinae are difficult to identify. To identify the relationships between the 15 Oncidiinae hybrids, eight regions of the  Onc . Gower Ramsey chloroplast genome were amplified by PCR for phylogenetic analysis. A total of 7042 bp derived from the eight regions could identify the relationships at the species level, which were supported by high bootstrap values. One particular 1846 bp region, derived from two PCR products ( trnH  GUG  - psbA  and  trnF  GAA - ndhJ ) was adequate for correct phylogenetic placement of 13 of the 15 varieties (with the exception of  Degarmoara  Flying High and  Odontoglossum  Violetta von Holm). Thus the chloroplast genome provides a useful molecular marker for species identifications.    Conclusion  In this report, we used  Phalaenopsis. aphrodite  as a prototype for primer design to complete the  Onc . Gower Ramsey genome sequence. Gene annotation showed that most of the  ndh  genes inOncidiinae, with the exception of  ndhE , are non-functional. This phenomenon was observed in all of the Oncidiinae species tested. The genes and chloroplast DNA regions that would be the most useful for phylogenetic analysis were determined to be the  trnH  GUG - psbA  and the  trnF  GAA - ndhJ  regions. We conclude that complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies in  Oncidium  with applications for breeding and variety identification.

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae