Meta-analysis reveals how mobs can alter gene expression in some insects

A grasshopper hatched in a crowded environment may look and behave differently than a grasshopper hatched in isolation, even though they have the same genes. The mechanism for this density-dependent phenomenon, called polyphenism, is well documented in aphids and grasshoppers, but how the genes regulate these traits has been unclear until now. Researchers from the University of Hiroshima analyzed data sets collected in previous studies to better understand how genes can influence each other to change their expression based on environmental conditions.

They published their findings on September 23 i Insects.

“Lice exhibit multiple wing types, and grasshoppers exhibit different body colors and behaviors,” said corresponding author Hidemasa Bono, a professor at Hiroshima University’s Graduate School of Integrated Sciences for Life. “These well-known agricultural pests are representative of insects that exhibit density-dependent plasticity. To reveal molecules common to all or multiple species that exhibit the same type of plasticity, we collected and reanalyzed publicly available RNA-sequencing data on aphids and grasshoppers.”

RNA sequencing data, called the transcriptome, is a collection of different expressed genes. It can also help identify new genes involved in producing specific traits. By performing a meta-analysis, researchers combine transcriptome results from multiple studies to see what the data says. In this study, researchers analyzed 66 public transcriptome datasets of seven species of aphids and grasshoppers.

“Meta-analysis is believed to be effective in providing additional information on density-dependent polyphenism because it can uncover new information that would not be found with conventional hypothesis-based research methods,” said first author Kouhei Toga, a researcher at the Ph.D. from Hiroshima University. integrated sciences for life. “This study is the first meta-analysis performed on datasets from two evolutionarily distant genera, and it identified many density-responsive genes that have been under-researched to elucidate the molecular mechanisms of density-dependent plasticity.”

Specifically, the researchers found that DNA replication, DNA metabolic processes, and the mitotic cell cycle were all enriched in response to crowded conditions. According to Toga, their results emphasize the importance of these processes – which have rarely been researched in this area – as regulatory mechanisms in research on density-dependent polyphenism.

They also found inconsistencies with some studies, including one that found a gene associated with pigmentation in more sociable grasshoppers was more expressed in isolated conditions. Compared with data from other studies, the researchers found that the gene fell into a category of other genes that up-regulated their expression during oxidative stress. According to Bono, oxidative stress is a more likely explanation for the high gene expression in solitary grasshoppers than under crowded conditions.

“We also found that changes in the neurological system can play an important role in inducing density-dependent phenotypic changes in two lineages,” Bono said, explaining that several genes that function in the nervous system that would lead to density-dependent behavioral changes increased under isolated conditions. conditions.

The results can be broadly applied to other species that exhibit density-dependent polyphenism due to the amount of data from so many studies, which serves as a cross-check of previous hypotheses and results, according to Toga.

“With the increase in public RNA sequencing data, a meta-analysis combining data from multiple studies has successfully provided new insights into targeted biological processes,” said Toga. “We hope that the functional analysis of the genes identified in this study will lead to the development of methods to control the growth of aphids and grasshoppers. We also hope to clarify how organisms respond and adapt to density by using meta -analysis on different species.”

The Innovation Center for Biodigital Transformation and the Japan Science and Technology Agency supported this research. The calculations for this work were performed on computers at Hiroshima University’s Genome Editing Innovation Center.

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Material supplied by Hiroshima University. Note: Content can be edited for style and length.

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