A new workflow for annotating gene function in insects

Genome sequencing, in which scientists use laboratory methods to determine the genetic makeup of a particular organism, is becoming common practice in insect research. A better understanding of insect biology helps scientists better manage insects, both those that are beneficial to the ecosystem and those that damage the food supply and threaten human health by carrying disease.

The researchers developed a workflow method called Fanflow4Insects that annotates gene functions in insects. In functional annotation, scientists gather information about the biological identity of a gene. The team’s new method uses transcribed sequence information as well as genomic and protein sequence databases. With Fanflow4Insects, the team annotated the functional information of the Japanese stick insect and silkworm, including gene expression as well as sequence analysis. The functional annotation information their workflow provides will greatly expand the possibilities of entomological research using genome editing.

The team, which includes scientists from Hiroshima University, Tokyo University of Agriculture and Technology, and the RIKEN Center for Integrative Medical Sciences, published their Fanflow4Insects method June 27 in the journal Insects.

Insects are so diverse and abundant that scientists need a way to study them on a large scale. This prompted scientists to begin work on sequencing the insect genome. As of May 2022, scientists have decoded and recorded the genomes of about 3,000 insect species. They also use long-read sequencing technology to further accelerate the pace of insect genome sequencing.

Next-generation sequencing has made it easier for researchers to decode the genomes of numerous insects along with their transcript sequences. However, the biological interpretation of these sequences remains the main bottleneck of transcriptome analysis. The transcriptome is the sum of an organism’s RNA molecules. Transcriptome analysis is an important first step in functional annotation, which serves as an important clue for selecting targets for genome editing.

Because some insects have genomes larger than the human genome, the difficult process of whole-genome sequencing is even more complicated. So scientists are using transcriptome sequencing with next-generation sequencing technology, also called RNA sequencing, as a tool to assess large genome-sized insects. With this powerful tool, scientists can effectively identify tens of thousands of possible genes in a specific tissue by collecting tens of millions of reads. They then assemble the gene sequences into transcription units for identification. But these types of analyzes depend on scientists having access to comprehensive datasets and their functional annotation. Databases exist, but they are unable to keep pace with the increase in insect genome sequencing.

As transcriptome analysis has become more popular, many research groups operate their own channels, with information on transcription units from different studies reported on a study-by-study basis. These pipelines are sets of algorithms used to process genome sequencing data. But scientists need a way to integrate the functional annotation from all the different groups doing this type of research into public databases.

In this current study, the research team used their newly developed Fanflow4Insects to create a functional annotation pipeline for the silkworm. The researchers then also tested Fanflow4Insects on the transcriptomes of the Japanese stick insect. “Functional annotation is one of the most important processes to accelerate target gene selection once the genome or transcriptome of a target organism has been decoded. The functional annotation information obtained from the Fanflow4Insects workflow will greatly expand the possibilities of entomological research using genome editing,” said Hidemasa Bono, a professor at the Graduate School of Integrated Life Sciences at Hiroshima University and first and corresponding author of the paper.

The Fanflow4Insects insect workflow is openly developed on GitHub and is freely available. In conjunction with expression-derived functional annotation, Fanflow4Insects data can be applied to the comparative study of insects with different phenotypes. “Using Fanflow4Insects, we will comment on insects that produce beneficial substances. The ultimate goal of this study is to make it possible to design molecular networks in insects using computer simulation,” Bono said.

Reference: Bono H, Sakamoto T, Kasukawa T, Tabunoki H. A systematic workflow of functional annotation for insects. Insects. 2022;13(7):586. doi: 10.3390/insects13070586

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