Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan.
PLoS One. 2012;7(4):e34738. doi: 10.1371/journal.pone.0034738. Epub 2012 Apr 4.
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.
文心兰属是一种重要的观赏植物，但对其功能基因组学的研究较为困难。香荚兰是一种生长迅速的文心兰亚属物种。其具有染色体数目低、基因组小、生长周期短以及能够在体外完成其生命周期等特点，使其成为兰花杂交的理想候选模型和亲本。尽管遗传信息仍然有限，但对其叶绿体基因组进行系统的分子分析可能会提供有用的遗传信息。通过结合细菌人工染色体 (BAC) 克隆和下一代测序 (NGS)，准确、高效且经济地对香荚兰的叶绿体 (cp) 基因组进行了测序。香荚兰的 cp 基因组与 Oncidium Gower Ramsey 和 Phalanopsis aphrodite 的相似度分别为 89%和 84%。比较这 3 个 cp 基因组，发现有 5 个区域表现出多样性。通过对隶属于 Epidendroideae 亚科的 19 个种进行 PCR 分析，在 Cymbidieae 族的 rps15-trnN 区域发现了一个保守缺失。由于台湾的商业文心兰品种有限，因此使用分子育种方法鉴定潜在亲本变得非常重要。为了证明香荚兰的分类地位与杂交亲和性之间的关系，对 36 种热带适应的文心兰亚属品种的 4 个 DNA 区域进行了分析。结果表明，trnF-ndhJ 和 trnH-psbA 适用于系统发育分析。尽管香荚兰的花形与文心兰相似，但它与 Rodriguezia 和 Tolumnia 的亲缘关系比文心兰更近。这些结果表明香荚兰的杂交亲和性，其 cp 基因组为文心兰的培育提供了重要信息。
