Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

Abstract

BackgroundOncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic identification very difficult. Molecular markers derived from the chloroplast genome can provide useful tools for phylogenetic resolution.ResultsThe complete chloroplast genome of the economically important Oncidium variety Onc. Gower Ramsey (Accession no. GQ324949) was determined using a polymerase chain reaction (PCR) and Sanger based ABI sequencing. The length of the Oncidium chloroplast genome is 146,484 bp. Genome structure, gene order and orientation are similar to Phalaenopsis, but differ from typical Poaceae, other monocots for which there are several published chloroplast (cp) genome. The Onc. Gower Ramsey chloroplast-encoded NADH dehydrogenase (ndh) genes, except ndhE, lack apparent functions. Deletion and other types of mutations were also found in the ndh genes of 15 other economically important Oncidiinae varieties, except ndhE in some species. The positions of some species in the evolution and taxonomy of Oncidiinae are difficult to identify. To identify the relationships between the 15 Oncidiinae hybrids, eight regions of the Onc. Gower Ramsey chloroplast genome were amplified by PCR for phylogenetic analysis. A total of 7042 bp derived from the eight regions could identify the relationships at the species level, which were supported by high bootstrap values. One particular 1846 bp region, derived from two PCR products (trnHGUG -psbA and trnFGAA-ndhJ) was adequate for correct phylogenetic placement of 13 of the 15 varieties (with the exception of Degarmoara Flying High and Odontoglossum Violetta von Holm). Thus the chloroplast genome provides a useful molecular marker for species identifications.ConclusionIn this report, we used Phalaenopsis. aphrodite as a prototype for primer design to complete the Onc. Gower Ramsey genome sequence. Gene annotation showed that most of the ndh genes inOncidiinae, with the exception of ndhE, are non-functional. This phenomenon was observed in all of the Oncidiinae species tested. The genes and chloroplast DNA regions that would be the most useful for phylogenetic analysis were determined to be the trnHGUG-psbA and the trnFGAA-ndhJ regions. We conclude that complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies in Oncidium with applications for breeding and variety identification.

The complete plastome sequence of the endangered orchid Kuhlhasseltia nakaiana (Orchidaceae)

“…A typical plant plastome contains 11 ndh family genes; the K. nakaiana plastome, however, contained only the ndhE gene, with the other 10 ndh genes pseudogenized or lost. These ndh gene losses are not unique to the K. nakaiana plastome and occur commonly in the plastomes of Orchidaceae plants (Chang et al 2006;Wu et al 2010;Lin et al 2015). In total, the plastome of K. nakaiana contained 103 unique genes including 69 protein-coding genes, 30 tRNA genes, and four rRNA genes.…”

The Complete Plastid Genome Sequence of Iris gatesii (Section Oncocyclus), a Bearded Species from Southeastern Turkey

“…Orchidaceae are early diverging within Asparagales (Pires et al 2006;Seberg et al 2012;Chen et al 2013) and are estimated to have a stem node age of 95.7 MYA and a crown node age of 51.6 MYA (Chen et al 2013). The orchid plastid genomes investigated to date lack all or some of their ndh genes or coding functions (Chang et al 2006;Wu et al 2010;Pan et al 2012;Yang et al 2013) and are unlikely to be typical for other members of Asparagales such as Iridaceae.…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…Chloroplast genomes have been successfully used in numerous phylogenetic studies of angiosperms [27,28]. To identify the phylogenetic position of the six Fritillaria species within the Liliaceae family, 74 protein-coding sequences shared by 11 cp genomes were aligned (Figure 7).…”