Comparative Chloroplast Genomes of Photosynthetic Orchids: Insights into Evolution of the Orchidaceae and Development of Molecular Markers for Phylogenetic Applications

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.

A molecular phylogeny of Chinese orchids

“…Within the higher epidendroids, support for the relationships of these clades is not high, and the sequences of certain genera are lacking; thus, the relationships among the tribes and monophylies of Epidendreae are not clearly refuted on the basis of the TL results. The topology of the RT is nearly consistent with previous molecular analyses (Górniak et al, ; Luo et al, ; Freudenstein & Chase, ; Givnish et al, ; Zhang et al, 2015a) and the classification of Chase et al () and the tribe and subtribe levels are successively sister to the next; thus, we chose the results of the RT to elucidate the arrangement of the suprageneric levels.…”

The use of next generation sequencing to solve phylogenetic incongruences in Orchidaceae Juss

“…We recovered approximately 132kb, after the exclusion of gaps, 310 representing 116 genes, seven pseudogenes, as well as regions with intergenic sequences and 311 introns with secondary structure. Compared to the reference annotation, seven genes 312 contained frameshifts that are usually associated with pseudogenisation and corresponded to 313 previously reported pseudogenised genes in orchids (Luo et al, 2014). 314…”

Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes

“…Several plastid regions, such as matK, atpB, psbB, psbC and rpoC1, have been used to identify phylogenetic relationships in orchid (Cameron 2004;Cameron and Carmen Molina 2006) and results are consistent with our analysis in these four orchids also. To test the efficiency of gene sequences 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 (including Dendrobium officinale Cypripedium macranthos) (Luo et al 2014). The haplotype (gene) diversity Hd was 1.00 and nucleotide diversity (per site) Pi (p) was 0.10560 in Dendrobium, which indicate that the genotype showing the genetic diversity.…”