Institute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwan.
Plant Sci. 2012 Jul;190:62-73. doi: 10.1016/j.plantsci.2012.04.001. Epub 2012 Apr 7.
The chloroplast genome of Phalaenopsis equestris was determined and compared to those of Phalaenopsis aphrodite and Oncidium Gower Ramsey in Orchidaceae. The chloroplast genome of P. equestris is 148,959 bp, and a pair of inverted repeats (25,846 bp) separates the genome into large single-copy (85,967 bp) and small single-copy (11,300 bp) regions. The genome encodes 109 genes, including 4 rRNA, 30 tRNA and 75 protein-coding genes, but loses four ndh genes (ndhA, E, F and H) and seven other ndh genes are pseudogenes. The rate of inter-species variation between the two moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The IR regions have a lower rate of nucleotide substitution (3.5-5.8-fold) and indels (4.3-7.1-fold) than single-copy regions. The intergenic spacers are the most divergent, and based on the length variation of the three intergenic spacers, 11 native Phalaenopsis orchids could be successfully distinguished. The coding genes, IR junction and RNA editing sites are relatively more conserved between the two moth orchids than between those of Phalaenopsis and Oncidium spp.
蝴蝶兰叶绿体基因组的测定及兰科植物的比较。蝴蝶兰的叶绿体基因组为 148959bp，一对反向重复序列（25846bp）将基因组分为大的单拷贝区（85967bp）和小的单拷贝区（11300bp）。基因组编码 109 个基因，包括 4 个 rRNA、30 个 tRNA 和 75 个蛋白编码基因，但丢失了四个 ndh 基因（ndhA、E、F 和 H），另外七个 ndh 基因是假基因。两种蝴蝶兰之间的种间变异率为单核苷酸替换的 0.74%（1107 个位点）和插入（161 个位点；1388bp）和缺失（189 个位点；1393bp）的 0.24%。IR 区的核苷酸替换率（3.5-5.8 倍）和插入缺失率（4.3-7.1 倍）均低于单拷贝区。基因间区的变异最大，根据三个基因间区的长度变化，成功区分了 11 种本地蝴蝶兰。与 Phalaenopsis 和 Oncidium spp 相比，编码基因、IR 连接区和 RNA 编辑位点在两种蝴蝶兰之间更为保守。
