Exploratory Analysis of Transposable Elements in the Partial Genome of Ludisia discolor (Orchidaceae)
Transposable elements (TEs) play an important role in the evolution of plant genomes as well as generating chromosomal mutations and allelic diversity. Advances in next generation sequencing (NGS) methods has enabled rapid generation of large amount of sequence data, especially useful for wild and understudied plants such as the Jewel orchid, Ludisia discolor (Ker Gawl.) A. Rich. (Orchidaceae). This orchid has been cultivated for more than 150 years for its attractive dark green-purple leaves with silver-red lateral veins. Illumina Miseq sequencing data ofL. discolor were subjected to TE analysis using open softwares such as like RepeatMasker, CENSOR, and MITE Digger to discover and analyze different families of TEs present in the partial genome of L. discolor. Interesting finds include identification and annotation of full length MITEs as well as possible discovery of SMART and TRIM elements, together with a number of solo LTRs. The total percentage of TEs in the partial genome of L. discolor is currently estimated at 16.95%, which is considerably low compared to model plants. Future works may include primer design and the development of molecular markers base on TEs from L. discolor.
Dr Sheh May Tam obtained her PhD in Plant Systematics and Evolution from the University of Cambridge, United Kingdom in 2002. Her research interest centers on the fields of plant evolutionary genetics and biodiversity – current investigations include both macro and micro-evolutionary studies involving the regulation of homeologous recombination in tomato and wild relatives, plant pollinator co-evolutionary study of Bulbophyllum spp.(Orchidaceae), genomics studies and marker development in Ludisia discolor, and Chiloschista sweelimii (Orchidaceae), miRNA regulation of lignin biosynthesis in Acacia mangium and mutagenesis study using transposable elements. She has worked in several academic institutes in France, the United States, and is currently a Senior Lecturer at the School of Biosciences, Taylor’s University, Malaysia.