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

Abstract

<p>Abstract</p> <p>Background</p> <p><it>Oncidium </it>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.</p> <p>Results</p> <p>The complete chloroplast genome of the economically important <it>Oncidium </it>variety <it>Onc</it>. Gower Ramsey (Accession no. GQ324949) was determined using a polymerase chain reaction (PCR) and Sanger based ABI sequencing. The length of the <it>Oncidium </it>chloroplast genome is 146,484 bp. Genome structure, gene order and orientation are similar to <it>Phalaenopsis</it>, but differ from typical Poaceae, other monocots for which there are several published chloroplast (cp) genome. The <it>Onc</it>. Gower Ramsey chloroplast-encoded <it>NADH dehydrogenase </it>(<it>ndh</it>) genes, except <it>ndhE</it>, lack apparent functions. Deletion and other types of mutations were also found in the <it>ndh </it>genes of 15 other economically important Oncidiinae varieties, except <it>ndhE </it>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 <it>Onc</it>. 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 (<it>trnH</it>^GUG-<it>psbA </it>and <it>trnF</it>^GAA-<it>ndhJ</it>) was adequate for correct phylogenetic placement of 13 of the 15 varieties (with the exception of <it>Degarmoara </it>Flying High and <it>Odontoglossum </it>Violetta von Holm). Thus the chloroplast genome provides a useful molecular marker for species identifications.</p> <p>Conclusion</p> <p>In this report, we used <it>Phalaenopsis. aphrodite </it>as a prototype for primer design to complete the <it>Onc</it>. Gower Ramsey genome sequence. Gene annotation showed that most of the <it>ndh </it>genes inOncidiinae, with the exception of <it>ndhE</it>, 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 <it>trnH</it>^GUG-<it>psbA </it>and the <it>trnF</it>^GAA-<it>ndhJ </it>regions. We conclude that complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies in <it>Oncidium </it>with applications for breeding and variety identification.</p