Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism

• Published in: BMC biology Vol. 20; no. 1; pp. 1 - 16
• Main Authors: Liu, Xuanzeng, Majid, Muhammad, Yuan, Hao, Chang, Huihui, Zhao, Lina, Nie, Yimeng, He, Lang, Liu, Xiaojing, He, Xiaoting, Huang, Yuan
• Format: Journal Article
• Language: English
• Published: London BioMed Central 28.10.2022; BioMed Central Ltd; BMC
• Subjects: Abundance; Analysis; Biomedical and Life Sciences; Comparative analysis; Copy number; Divergence; Evolutionary genetics; Evolutionary Genomics; Genome size; Genomes; Gigantism; Grasshopper; Grasshoppers; Life Sciences; Methylase; Parasites; piRNA silencing; Research Article; Ribonucleic acid; RNA; RNA sequencing; RNA-mediated interference; TE transcripts; Transposable elements; Transposition; Transposons; China; Genome size; TE transcripts; piRNA silencing; Grasshopper; Transposable elements
• ISSN: 1741-7007; 1741-7007
• DOI: 10.1186/s12915-022-01441-w

Background Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae ( Locusta migratoria manilensis ♀1C = 6.60 pg, Angaracris rhodopa ♀1C = 16.36 pg) to ascertain the influence of piRNAs. Results We discovered that repetitive sequences accounted for 74.56% of the genome in A. rhodopa, more than 56.83% in L. migratoria , and the large-genome grasshopper contained a higher TEs proportions. The comparative analysis revealed that 41 TEs (copy number > 500) were shared in both species. The two species exhibited distinct “landscapes” of TE divergence. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. We found that TE transcript abundance was higher in the large-genome grasshopper and the TE-derived piRNAs abundance was lower than in the small-genome grasshopper. In addition, we found that the piRNA methylase HENMT, which is underexpressed in the large-genome grasshopper, impedes the piRNA silencing to a lower level. Conclusions Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway (Ping-Pong cycle) in the gigantic genome grasshopper is underexpressed. We hypothesize that low-level piRNA silencing unbalances the original positive correlation between TEs and piRNAs, and triggers TEs to proliferate out of control, which may be one of the reasons for the gigantism of grasshopper genomes.