Introduction #

Transposable elements (TEs) (otherwise transposons/jumping genes) are the repeated DNA sequences widely present in eukaryote genomes, especially higher plants. It creates more complex nature for de novo assembly and structural annotation. Hence, predicting TEs in genome sequence is more complicated based on specific constrains.

TE classification #

It has been reported that almost all eukaryote genome have repeat regions. Besides, from the available genomic information, there are about 20~80% repeat region has been reported in plant genome, whereas 3~20% and 3~45% reported in fungal genome metazoans, respectively. Based on the conservation and similarity, repeats were unified with some standards nomenclature. Initial classification was done by Finnegan in 1989, described in RNA (Class I: retrotransposons – Copy and paste) and DNA (Class II: DNA transposons – Cut and paste). Later, in 2007 Thomas Wiker group has classified based on the hierarchical structure; such as class, subclass, order, superfamily, family and subfamily which is similar to phylogenetics.

Figure 1 : Classification of TEs 1

Prediction Tool #

There are about 30 computational TE detection tools available.2

References: #

1 Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., et al. 2007 A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8, 973-982.

2 Bergman, C.M. & Quesneville, H. 2007 Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics 8, 382-392. (doi:10.1093/bib/bbm048).