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Oncidium  is an important ornamental plant but the study of its functional genomics is difficult.  Erycina pusilla  is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle  in vitro  make  E. pusilla  a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of  E. pusilla  was sequenced accurately, efficiently and economically. The cp genome of  E. pusilla  shares 89 and 84% similarity with  Oncidium  Gower Ramsey and  Phalanopsis aphrodite , respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the  rps15-trnN  region of the Cymbidieae tribe. Because commercial  Oncidium  varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of  E. pusilla , 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that  trnF - ndhJ  and  trnH - psbA  were suitable for phylogenetic analysis.  E. pusilla  proved to be phylogenetically closer to  Rodriguezia  and  Tolumnia  than  Oncidium , despite its similar floral appearance to  Oncidium . These results indicate the hybrid compatibility of  E. pusilla , its cp genome providing important information for  Oncidium  breeding.

Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding