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

The horizontal axis shows gene sequencing based on the method developed in our laboratory for meta-analysis of RNA sequencing data. The vertical axis shows the values ​​used to rank the genes. High-order and low-order genes indicate genes that are up-regulated in response to high and low intensities, respectively. Gene names are annotated next to the graphs for previously reported density responsive genes. In addition, genes not reported as density-sensitive genes were also included in high- and low-order genes. Credit: Kouhei Toga, Hiroshima University

A locust that hatches in a crowded environment may look and behave differently from a locust that hatches alone, even if they have the same genes. The mechanism of this density-dependent phenomenon, called polyphenism, is well documented in both aphids and grasshoppers, but how genes regulate these traits has remained elusive until now.

Researchers from Hiroshima University analyzed datasets collected from previous studies to better understand how genes can influence each other to change their expression depending on environmental conditions. They published their results on September 23. Vermin.

“Aphids display multiple wing types, and grasshoppers display different body colors and behaviors,” said corresponding author Hidemasa Bono, a professor at Hiroshima University’s Institute of Integrated Sciences. “These well-known agricultural pests represent insects that exhibit density-dependent plasticity. We collected and reanalyzed publicly available RNA-sequencing data of aphids and grasshoppers to reveal molecules common to all or multiple species that exhibit this same type of plasticity.”

RNA sequencing data, called transcriptome, is a collection of various expressed genes. It can also help identify new genes involved in producing certain traits. Researchers perform a meta-analysis, combining transcriptome results from multiple studies to see what the data are saying. In this study, the researchers analyzed 66 general transcriptome datasets from seven species of aphids and grasshoppers.

“Meta-analysis is thought to be effective in providing additional information about density-dependent polyphenism because it can reveal new information that cannot be found with traditional hypothesis-driven research methods,” said first author Kouhei Toga, a researcher at Hiroshima University Graduate School. Integrated Sciences for Life.

“This study is the first meta-analysis conducted on datasets of two evolutionarily distant lineages and has identified many density-sensitive genes that are rarely the focus of research aimed at elucidating the molecular mechanisms of density-dependent plasticity.”

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

They also found inconsistencies with some studies, including a study that found a pigmentation-related gene to be expressed higher in isolated conditions in more herding locusts. Compared with data from other studies, the researchers found that the gene fit within the category of other genes that upregulate their expression when under oxidative stress. According to Bono, oxidative stress is a more likely explanation for high gene expression in locust locusts than in crowded conditions.

“We found that neurological system modifications can play an important role in triggering density-dependent phenotypic changes in the two lineages,” Bono said. conditions.

According to Toga, the findings are generally applicable to other species that exhibit density-dependent polyphenism, due to the large amount of data from many studies that serve as a cross-check of previous hypotheses and results.

“A meta-analysis combining data from multiple studies with growing publicly available RNA sequencing data was able to provide new insights into targeted biological processes,” Toga said. Said.

“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 applying meta-analysis to various species.”

More information:
Kouhei Toga et al., Meta-Analysis of Transcriptomes in Insects Showing Density-Related Polyphenism, Vermin (2022). DOI: 10.3390/insects13100864

Provided by Hiroshima University

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