Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

Abstract

The production of genome sequences has led to another important advance in their annotation, which is closely linked to the exact determination of their content in terms of repeats, among which are transposable elements (TEs). The evolutionary implications and the presence of coding regions in some TEs can confuse gene annotation, and also hinder the process of genome assembly, making particularly crucial to be able to annotate and classify them correctly in genome sequences. This review is intended to provide an overview as comprehensive as possible of the automated methods currently used to annotate and classify TEs in sequenced genomes. Different categories of programs exist according to their methodology and the repeat, which they can identify. I describe here the main characteristics of the programs, their main goals and the difficulties they can entail. The drawbacks of the different methods are also highlighted to help biologists who are unfamiliar with algorithmic methods to understand this methodology better. Globally, using several different programs and carrying out a cross comparison of their results has the best chance of finding reliable results as any single program. However, this makes it essential to verify the results provided by each program independently. The ideal solution would be to test all programs against the same data set to obtain a true comparison of their actual performance.

msechBari, a new MITE-like element inDrosophila sechelliarelated to theBaritransposon

“…Accordingly, the groupings of sequences in the network, represented by large circles, indicate that the sequences are identical ; therefore, these sequences are very recent and have not had sufficient time to diverge. Similar events have been reported for other transposable elements (Yang et Konovalov et al, 2010 ;Lerat, 2010) and MITE-like sequences in different organisms (Jiang et al, 2003 ;Chen et al, 2008;Zhou et al, 2008 ;Han et al, 2010 ;Hikosaka et al, 2011). This recent origin is also supported by the average time of origin of the insertions of each subfamily, 155 000 years (msechBari1) and 127 000 years (msechBari2).…”

Mammalian Endogenous Retroviruses

“…This has led to the completion of multiple genome-sequencing projects. Simultaneously, a variety of in silico techniques for identifying and annotating potential ERVs have been developed (20). These entail searches for conserved sequences and/or sequence motifs organized in the same manner as exogenous retroviruses (21).…”

Organization and evolution of transposable elements along the bread wheat chromosome 3B

“…A high-quality TE prediction and annotation is essential to prevent mis-annotation of functional genes and to understand the biology of genomes [29]. Different strategies have been developed, including similarity search against databanks of known TE sequences, de novo repeat detection, k-mer-based counting, and structural motif detection (reviewed in [30]). Despite the development of many dedicated bioinformatic tools, precise TE modeling in complex (>1 Gb) genomes, such as in wheat or maize, is a tour de force.…”