Large-Scale Transcriptome Analysis of Retroelements in the Migratory Locust, Locusta migratoria

Feng Jiang,Xianhui Wang,Meiling Yang,Le Kang,Wei Guo,Jialin Charles Zheng

doi:10.1371/journal.pone.0040532

Abstract

BackgroundRetroelements can successfully colonize eukaryotic genome through RNA-mediated transposition, and are considered to be some of the major mediators of genome size. The migratory locust Locusta migratoria is an insect with a large genome size, and its genome is probably subject to the proliferation of retroelements. An analysis of deep-sequencing transcriptome data will elucidate the structure, diversity and expression characteristics of retroelements.ResultsWe performed a de novo assembly from deep sequencing RNA-seq data and identified 105 retroelements in the locust transcriptome. Phylogenetic analysis of reverse transcriptase sequences revealed 1 copia, 1 BEL, 8 gypsy and 23 non-long terminal repeat (LTR) retroelements in the locust transcriptome. A novel approach was developed to identify full-length LTR retroelements. A total of 5 full-length LTR retroelements and 2 full-length non-LTR retroelements that contained complete structures for retrotransposition were identified. Structural analysis indicated that all these retroelements may have been activated or deprived of retrotransposition activities very recently. Expression profiling analysis revealed that the retroelements exhibited a unique expression pattern at the egg stage and showed differential expression profiles between the solitarious and gregarious phases at the fifth instar and adult stage.ConclusionWe hereby present the first de novo transcriptome analysis of retroelements in a species whose genome is not available. This work contributes to a comprehensive understanding of the landscape of retroelements in the locust transcriptome. More importantly, the results reveal that non-LTR retroelements are abundant and diverse in the locust transcriptome.

Highlights

In insects, genome sizes vary across two orders of magnitude, i.e., from less than 100 megabases to larger than 10 gigabases (Gb) [1]
The scaffolds inferred from the paired-end information were verified by translation mapping methods, which search orthologous regions in the protein sequences from Repbase using translated contigs
Given that the structure signatures are almost absent in the transcriptome, retroelements were sought by an approach that relied on homology searching of the known retrotransposon proteins using the protein-based RepeatMasking program to identify transcripts that contain an inner region of retrotransposon homologous proteins

Summary

Introduction

Genome sizes vary across two orders of magnitude, i.e., from less than 100 megabases to larger than 10 gigabases (Gb) [1]. Emerging genomic data from genome sequencing projects in different organisms show that TEs constitute a large portion of eukaryotic genomes (3%– 45% in metazoans) [3]. These elements appear to have very similar structures, basically containing genes responsible for their transposition. To attenuate genome size expansion via retroelement proliferation, inactive retroelements eventually decay and are excised from the genome under relaxed selection [6] Due to their ability to proliferate and their susceptibility to decay, retroelements appear to have a large impact on genome size variations [2]. An analysis of deep-sequencing transcriptome data will elucidate the structure, diversity and expression characteristics of retroelements

Methods

Results

Conclusion