《Trends in Plant Science-2016-Ragupathy-Arguments for》.pdf

Opinion Arguments for standardizing transposable element annotation in plant genomes 1,2 1 1,2 Raja Ragupathy , Frank M. You , and Sylvie Cloutier 1 Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada 2 Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada Whole genome sequence assemblies have been gener- genome sequence assemblies have been generated for ated for many plants. Annotation of transposable ele- many agriculturally important plants. Next-generation ments (TEs), which constitute the major proportion of sequencing (NGS) platforms with their steadily decreasing genomes and play a significant role in epigenome altera- cost and increasing throughput [4] have paved the way for tions under stress, has not been given equal importance the generation of 22 dicot and 8 monocot whole genome to that of genes. In this opinion article, we argue that the sequence assemblies to date (Table 1). Most of these gen- lack of focus dedicated to the fine-scale characterization omes were sequenced and assembled using a whole-ge- of repeat fractions and the absence of consistent meth- nome shotgun strategy without a clone-based physical map ods for their annotation impede our ability to critically which resulted in generally poorer quality de novo assem- understand the influence of TEs on the epigenome with blies with gaps and misassemblies, mainly due to the implications in gene expression and non-Mendelian in- inability of the short reads (35–400 bp) to adequately heritance. Major structural changes oc