The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny

Abstract

Moth orchids (Phalaenopsis) are among the top-traded blooming potted plants in the world. To explore mitochondrial DNA (mtDNA) markers for species identification, we located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana and then pre-screened them for polymorphic markers by their comparison with corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish 15 endemic moth orchids. Five most variable markers with polymorphic information content (PIC) ≥ 0.7 could be combined to classify 18 of 19 endemic moth orchids including parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids, evolutionary hotspots, such as variable simple sequence repeats and minisatellite repeats, were identified as useful markers. Furthermore, a marker technology was applied to reveal the maternal inheritance mode of mtDNA in the moth orchids. Moreover, phylogenetic analysis indicates that the mtDNA was nonmonophyletic below the Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.

Whole plastid transcriptomes reveal abundant RNA editing sites and differential editing status in Phalaenopsis aphrodite subsp. formosana

“…The Orchidaceae family contains approximately 25,000 species and represents one of the most diverse families in flowering plants (Dressler 2005 ). The Phalaenopsis (moth orchids) genus comprises approximately 66 endemic species (Christenson 2001 ; Lin et al 2016 ). Moth orchids are among the top-traded blooming potted plants in the world, with more than 32,000 hybrids bred and registered in the Royal Horticultural Society (Lin et al 2015a , b ; Liu et al 2016 ).…”

Research Article PhalDB:A comprehensive database for molecular mining of the <i>Phalaenopsis</i> genome, transcriptome and miRNome

“…The Phalaenopsis (moth orchid) genus consists of about 66 species distributed throughout tropical Asia, and these are prevalent ornamental plants because of their stylish appearance, the ease of production, low maintenance and prolonged flower longevity (Christenson 2001). Potted Phalaenopsis is one of the best outstanding orchids with more than 32,000 hybrids bred and is of great economic significance yielding more than 500 million US dollars annually for the floral industry (Lin et al, 2016). Phalaenopsis species have the same chromosome number (2n = 2x = 38), with chromosome sizes ranging from 1.5 to 3.5 µm and a predicted genome size of nearly 1.5 gigabases (Arends 1970 andLin et al, 2001).…”