Characterization of Three Novel SINE Families with Unusual Features in Helicoverpa armigera

Jianjun Wang,Zan Zhang,Aina Wang,Zhaojun Han,Xianchun Li,Fei Li,Mary Bryk

doi:10.1371/journal.pone.0031355

Abstract

Although more than 120 families of short interspersed nuclear elements (SINEs) have been isolated from the eukaryotic genomes, little is known about SINEs in insects. Here, we characterize three novel SINEs from the cotton bollworm, Helicoverpa armigera. Two of them, HaSE1 and HaSE2, share similar 5′ -structure including a tRNA-related region immediately followed by conserved central domain. The 3′ -tail of HaSE1 is significantly similar to that of one LINE retrotransposon element, HaRTE1.1, in H. armigera genome. The 3′ -region of HaSE2 showed high identity with one mariner-like element in H. armigera. The third family, termed HaSE3, is a 5S rRNA-derived SINE and shares both body part and 3′-tail with HaSE1, thus may represent the first example of a chimera generated by recombination between 5S rRNA and tRNA-derived SINE in insect species. Further database searches revealed the presence of these SINEs in several other related insect species, but not in the silkworm, Bombyx mori, indicating a relatively narrow distribution of these SINEs in Lepidopterans. Apart from above, we found a copy of HaSE2 in the GenBank EST entry for the cotton aphid, Aphis gossypii, suggesting the occurrence of horizontal transfer.

Highlights

Transposable elements (TEs) form a substantial fraction of eukaryotic genomes and are categorized based on their mode of transposition as class-I elements or retrotransposons and class-II elements or DNA transposons [1]
A typical short interspersed nuclear elements (SINEs) is composed of three distinct regions: a 59 terminal RNA-related region which contains an internal RNA polymerase III (Pol III) promoter, a RNA-unrelated region, and the 39 tail region that is recognized by the reverse transcriptase (RT) of autonomous partner long interspersed nuclear elements (LINEs) during retrotransposition [3]
A novel tRNA-derived SINE family, designated as HaSE1, was identified by genome walking and subsequent database searches

Summary

Introduction

Transposable elements (TEs) form a substantial fraction of eukaryotic genomes and are categorized based on their mode of transposition as class-I elements or retrotransposons and class-II elements or DNA transposons [1]. Copy and paste retrotransposons replicate via an RNA intermediate, which is reverse transcribed prior to its reintegration into the genome, whereas cut and paste DNA transposons move through a DNA intermediate. Retrotransposons are the most widespread and enriched class of eukaryotic transposable elements, and can usually be classified into several groups by their replication strategy and structure, including long terminal repeat (LTR) elements, long interspersed nuclear elements (LINEs), and short interspersed nuclear elements (SINEs) [2]. A typical SINE is composed of three distinct regions: a 59 terminal RNA-related region (the head) which contains an internal RNA polymerase III (Pol III) promoter, a RNA-unrelated region (the body), and the 39 tail region that is recognized by the reverse transcriptase (RT) of autonomous partner LINEs during retrotransposition [3]

Methods

Results

Conclusion