Diversity of short interspersed nuclear elements (SINEs) in lepidopteran insects and evidence of horizontal SINE transfer between baculovirus and lepidopteran hosts

Guangjie Han,Jianjun Wang,Xiangkun Meng,Heng Jiang,Nan Zhang,Jian Xu,Yang Zheng,Kun Qian

doi:10.1186/s12864-021-07543-z

Guangjie Han, Jianjun Wang + Show 6 more

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https://doi.org/10.1186/s12864-021-07543-z

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Journal: BMC Genomics	Publication Date: Mar 31, 2021
Citations: 5	License type: open-access

Affiliation: Yangzhou University

Abstract

BackgroundShort interspersed nuclear elements (SINEs) belong to non-long terminal repeat (non-LTR) retrotransposons, which can mobilize dependent on the help of counterpart long interspersed nuclear elements (LINEs). Although 234 SINEs have been identified so far, only 23 are from insect species (SINEbase: http://sines.eimb.ru/).ResultsHere, five SINEs were identified from the genome of Plutella xylostella, among which PxSE1, PxSE2 and PxSE3 were tRNA-derived SINEs, PxSE4 and PxSE5 were 5S RNA-derived SINEs. A total of 18 related SINEs were further identified in 13 lepidopteran insects and a baculovirus. The 3′-tail of PxSE5 shares highly identity with that of LINE retrotransposon, PxLINE1. The analysis of relative age distribution profiles revealed that PxSE1 is a relatively young retrotransposon in the genome of P. xylostella and was generated by recent explosive amplification. Integration pattern analysis showed that SINEs in P. xylostella prefer to insert into or accumulate in introns and regions 5 kb downstream of genes. In particular, the PxSE1-like element, SlNPVSE1, in Spodoptera litura nucleopolyhedrovirus II genome is highly identical to SfSE1 in Spodoptera frugiperda, SlittSE1 in Spodoptera littoralis, and SlituSE1 in Spodoptera litura, suggesting the occurrence of horizontal transfer.ConclusionsLepidopteran insect genomes harbor a diversity of SINEs. The retrotransposition activity and copy number of these SINEs varies considerably between host lineages and SINE lineages. Host-parasite interactions facilitate the horizontal transfer of SINE between baculovirus and its lepidopteran hosts.

Highlights

Short interspersed nuclear elements (SINEs) belong to non-long terminal repeat retrotransposons, which can mobilize dependent on the help of counterpart long interspersed nuclear elements (LINEs)
While mammalian SINEs, such as B1 and Alu, are originated from 7SL RNAs, other eukaryotes primarily harbor tRNA-like SINEs [4], and SINEs originated from 5S rRNA have been found in zebrafish, fruit bats, and springhare [5, 6]
Highly identical conserved central domains among different SINEs in the same species suggests that the conserved central domain may originated from the same LINE family and has been under strong selective constraint, which is important for reverse transcription

Summary

Introduction

Short interspersed nuclear elements (SINEs) belong to non-long terminal repeat (non-LTR) retrotransposons, which can mobilize dependent on the help of counterpart long interspersed nuclear elements (LINEs). SINEs derived from small nuclear RNA (snRNA) (SINEU) and the 3′-end of the large ribosomal subunit (LSU or 28S rDNA) (SINE28) have been identified in avian, crocodilian and mammalian genomes, respectively [7,8,9]. The characteristic features of SINEs include a 5′ terminal RNArelated region which contains an internal Pol III promoter, a central region, and a 3′-tail that is of variable length and recognized by the reverse transcriptase (RT) of autonomous partner long nuclear interspersed element (LINE) during retrotransposition [3]. The SINEs promoters originated from tRNA and 7SL RNA comprise box A and B motif, whereas 5S rRNA-derived SINE promoters have three boxes such as A, IE and C [10]

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