Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding

• Published in: PloS one 2012-04, Vol.7 (4), p.e34738-e34738
• Main Authors: Pan, I-Chun, Liao, Der-Chih, Wu, Fu-Huei, Daniell, Henry, Singh, Nameirakpam Dolendro, Chang, Chen, Shih, Ming-Che, Chan, Ming-Tsair, Lin, Choun-Sea
• Format: Article
• Language: English
• Subjects: Agricultural biotechnology; Agriculture; Analysis; Bacterial artificial chromosomes; Base Sequence; Biodiversity; Biology; Breeding; Breeding methods; Chloroplasts; Chromosome number; Cladistic analysis; Clonal deletion; Cloning; Compatibility; Deoxyribonucleic acid; DNA; Epidendroideae; Erycina; Erycina pusilla; Evolution; Flowers & plants; Gene sequencing; Genes; Genetic analysis; Genetic aspects; Genetic engineering; Genome Size; Genome, Chloroplast; Genomes; Genomics; Hybridization; Hybrids; Information systems; Life cycle; Life cycle engineering; Life cycles; Medical screening; Molecular biology; Molecular Sequence Data; Nucleotide sequence; Oncidium; Orchidaceae; Orchidaceae - genetics; Ornamental plants; Parents; Phalaenopsis aphrodite; Phylogenetics; Phylogeny; Plant breeding; Polymerase chain reaction; Population genetics; Sequence Analysis, DNA - methods; Species diversity; Studies
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0034738

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.