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. 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. Here 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. Our 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.

Transposons are often regulated by their hosts, and as a result, there are transposons with several mutations within their host organisms. To gain insight into the patterns of the variations, nucleotide substitutions and indels of transposons were analysed in Chilo suppressalis Walker. The CsuPLE1.1 is a member of the piggyBac-like element (PLE) family, which belongs to the DNA transposons, and the Csu-Ty3 is a member of the Ty3/gypsy family, which belongs to the RNA transposons. Copies of CsuPLE1.1 and Csu-Ty3 were cloned separately from different C. suppressalis individuals, and then multiple sequence alignments were performed. There were numerous single-base substitutions in CsuPLE1.1 and Csu-Ty3, but only a few insertion and deletion mutations. Similarly, in both transposons, the occurring frequencies of transitions were significantly higher than transversions (p ≤ 0.01). In the single-base substitutions, the most frequently occurring base changes were A→G and T→C in both types of transposons. Additionally, single-base substitution frequencies occurring at positions 1, 2 or 3 (pos1, pos2 or pos3) of a given codon in the element transposase were not significantly different. Both in CsuPLE1.1 and Csu-Ty3, the patterns of nucleotide substitution had the same characteristics and nucleotide mutations were biased toward GC. This research provides a perspective on the understanding of transposon mutation patterns.

Survival and adaptation to seasonal changes are challenging for insects. Many temperate insects such as the rice stem borer (Chilo suppressalis) overcome the adverse situation by entering diapause, wherein development changes dynamically occur and metabolic activity is suppressed. The photoperiod and temperature act as major environmental stimuli of diapause. However, the physiological and molecular mechanisms that interpret the ecologically relevant environmental cues in ontogenetic development during diapause termination are poorly understood. Here, we used genome-wide high-throughput RNA-sequencing to examine the patterns of gene expression during diapause termination in C. suppressalis. Major shifts in biological processes and pathways including metabolism, environmental information transmission, and endocrine signalling were observed across diapause termination based on over-representation analysis, short time-series expression miner, and gene set enrichment analysis. Many new pathways were identified in diapause termination including circadian rhythm, MAPK signalling, Wnt signalling, and Ras signalling, together with previously reported pathways including ecdysteroid, juvenile hormone, and insulin/insulin-like signalling. Our results show that convergent biological processes and molecular pathways of diapause termination were shared across different insect species and provided a comprehensive roadmap to better understand diapause termination in C. suppressalis.