LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes.

Fan-Chun Zeng,You-Jie Zhao,Que-Jie Zhang,Li-Zhi Gao

doi:10.3389/fpls.2017.00402

Abstract

The amplification and recombination of long terminal repeat (LTR) retrotransposons have proven to determine the size, organization, function, and evolution of most host genomes, especially very large plant genomes. However, the limitation of tools for an efficient discovery of structural complexity of LTR retrotransposons and the nested insertions is a great challenge to confront ever-growing amount of genomic sequences for many organisms. Here we developed a novel software, called as LTRtype, to characterize different types of structurally complex LTR retrotransposon elements as well as nested events. This system is capable of rapidly scanning large-scale genomic sequences and appropriately characterizing the five complex types of LTR retrotransposon elements. After testing on the Arabidopsis thaliana genome, we found that this program is able to properly annotate a large number of structurally complex elements as well as the nested insertions. Thus, LTRtype can be employed as an automatic and efficient tool that will help to reconstruct the evolutionary history of LTR retrotransposons and better understand the evolution of host genomes. LTRtype is publicly available at: http://www.plantkingdomgdb.com/LTRtype/index.html.

Highlights

It has long been recognized that transposable elements compose an important fraction of most eukaryote genomes
long terminal repeat (LTR) retrotransposons are prevalent in most plant genomes, where they appear to be the major determinant of the tremendous variation in genome size (Wessler, 2006; Wicker et al, 2007; Wendel et al, 2016)
LTR retrotransposons are a class of mobile genetic elements containing two identical or similar long terminal repeats (LTRs) and one internal region (IN) between them, which are transposed through the reverse transcription of an RNA template via “copy-and-paste” in the genome

Summary

INTRODUCTION

It has long been recognized that transposable elements compose an important fraction of most eukaryote genomes. Most extensively implemented approaches of LTR retrotransposon identification were based on similarity searches against a target genome These tools, such as REPuter (Kurtz et al, 2001), RECON (Bao and Eddy, 2002), RAP (Campagna et al, 2005), PILER (Edgar and Myers, 2005), RepeatMasker and LTR Annotator (You et al, 2015), are able to detect repeat sequences in the genome, but they incorporated almost no defragmentation and have definitely resulted in the overestimated number of LTR retrotransposons. We developed a novel software program, named LTRtype, for the purpose of proficient discovery of diverse types of the structurally complex LTR retrotransposons (Figure 1) and nested insertions (Figure 2) in large quantities of genomic sequences. The program LTRtype reported here is able to proficiently mine increasingly sequenced genomes by using multithreading technologies, and provides a convenient and friendly service for users

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION