Abstract
BackgroundTransposable elements (TEs, transposons) are mobile genetic DNA sequences. TEs can insert copies of themselves into new genomic locations and they have the capacity to multiply. Therefore, TEs have been crucial in the shaping of hosts’ current genomes. TEs can be utilized as genetic markers to study population genetic diversity. The rice stem borer Chilo suppressalis Walker is one of the most important insect pests of many subtropical and tropical paddy fields. This insect occurs in all the rice-growing areas in China. This research was carried out in order to find diversity between C. suppressalis field populations and detect the original settlement of C. suppressalis populations based on the piggyBac-like element (PLE). We also aim to provide insights into the evolution of PLEs in C. suppressalis and the phylogeography of C. suppressalis.ResultsHere we identify a new piggyBac-like element (PLE) in the rice stem borer Chilo suppressalis Walker, which is called CsuPLE1.1 (GenBank accession no. JX294476). CsuPLE1.1 is transcriptionally active. Additionally, the CsuPLE1.1 sequence varied slightly between field populations, with polymorphic indels (insertion/deletion) and hyper-variable regions including the identification of the 3′ region outside the open reading frame (ORF). CsuPLE1.1 insertion frequency varied between field populations. Sequences variation was found between CsuPLE1 copies and varied within and among field populations. Twenty-one different insertion sites for CsuPLE1 copies were identified with at least two insertion loci found in all populations.ConclusionsOur results indicate that the initial invasion of CsuPLE1 into C. suppressalis occurred before C. suppressalis populations spread throughout China, and suggest that C. suppressalis populations have a common ancestor in China. Additionally, the lower reaches of the Yangtze River are probably the original settlement of C. suppressalis in China. Finally, the CsuPLE1 insertion site appears to be a candidate marker for phylogenetic research of C. suppressalis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12867-014-0028-y) contains supplementary material, which is available to authorized users.
Highlights
Transposable elements (TEs, transposons) are mobile genetic DNA sequences
As in other piggyBac-like element (PLE), the CsuPLE1.1 was inserted into typical tetranucleotide target-site TTAA duplications and flanked by a sequence (912 bp at 5′-end and 576 bp at 3′) that was not significantly homologous to any gene sequences in the GenBank
We identified another potentially active PLE. This PLE has the intact structure of a piggyBac transposon, including TTAA insertion sites, 13 bp inverted terminal repeats (ITRs), 25 bp subterminal inverted repeats, and a single open reading frame (ORF) encoding a transposase of 505 amino acids with a perfect “DDD-motif”
Summary
Transposable elements (TEs, transposons) are mobile genetic DNA sequences. TEs can insert copies of themselves into new genomic locations and they have the capacity to multiply. The rice stem borer Chilo suppressalis Walker is one of the most important insect pests of many subtropical and tropical paddy fields. Transposable elements (TEs, transposons) are mobile genetic DNA sequences, and they are found in the genomes of most eukaryotes [1,2]. The piggyBac element, which is a class II transposon, was originally discovered in the TN-368 cell line of the cabbage looper moth Trichoplusia ni [8,9]. It transposes via a “cut-and-paste” mechanism, inserting exclusively at 5′-TTAA-3′ tetranucleotide target sites and excising with precision, leaving no footprint [10]. PLEs are highly divergent and can be classified into three main classes, namely by high sequence similarity to IFP2, moderate sequence similarity to IFP2 and very distantly related ancient elements [14]
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