Abstract
The orchid family Orchidaceae is one of the largest angiosperm families, including many species of important economic value. While chloroplast genomes are very informative for systematics and species identification, there is very limited information available on chloroplast genomes in the Orchidaceae. Here, we report the complete chloroplast genomes of the medicinal plant Dendrobium officinale and the ornamental orchid Cypripedium macranthos, demonstrating their gene content and order and potential RNA editing sites. The chloroplast genomes of the above two species and five known photosynthetic orchids showed similarities in structure as well as gene order and content, but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy region underwent expansion or contraction among Orchidaceae. The AT-rich regions of the ycf1 gene in orchids could be linked to the recombination of inverted repeat/small single-copy junctions. Relative species in orchids displayed similar patterns of variation in ndh gene contents. Furthermore, fifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes (accD, ccsA, matK, and ycf1) were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family.
Highlights
The orchid family Orchidaceae is one of the two largest families of flowering plants, with over 25,000 species [1] and five recognized subfamilies (Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae) [2]
Sequencing and genome assembly The raw Illumina paired-end sequencing of D. officinale produced 350 Mb of data
The average coverage depth was 1,4006. These scaffolds were used for the following assembly
Summary
The orchid family Orchidaceae is one of the two largest families of flowering plants, with over 25,000 species [1] and five recognized subfamilies (Apostasioideae, Cypripedioideae, Epidendroideae, Orchidoideae, and Vanilloideae) [2]. A large number of orchids have significant economic value [3]. Some cultivars have been used as cut flowers or potted plants, while others can be utilized as food or medicine because of their nutritious or medical efficacy. Overexploitation and habitat destruction have threatened the survival of many wild orchid species. Numerous cultivated varieties and crossbreeds have been developed worldwide. Molecular information on orchids is of interest for the study of systematics, and for species conservation and flower cultivation
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