Wednesday, November 30, 2022

Scientists expand entomological research using genome editing

Genome sequencing, where scientists use laboratory methods to determine the genetic makeup of a specific organism, is becoming a common practice in insect research. A greater understanding of insect biology helps scientists better manage insects that are beneficial to ecosystems and those that damage the food supply and threaten human health with diseases.

Researchers have developed a work-flow method, called FanFlow4Pest, that explains gene functions in insects. In functional annotation, scientists collect information about the biological identity of a gene. The team’s new method uses genome and protein sequence databases along with transcribed sequence information. With Fanflow4Insects, the team has annotated the functional information of the Japanese stick moth and silkworm, including gene expression as well as sequence analysis. The functional annotation information provided by their workflow will expand the possibilities of entomology research using genome editing.

The team, along with scientists from Hiroshima University, Tokyo University of Agriculture and Technology and the RIKEN Center for Integrative Medical Sciences, have published their FanFlow 4 insect method on June 27 in the journal Pest.

Insects are so diverse and abundant that scientists need a way to study them on a larger scale. This is why scientists began work on sequencing the genomes of insects. By May 2022, scientists had decoded and registered the genomes of nearly 3000 insect species. They are also using 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 many insects along with their transcript sequences. However, biological interpretation of these sequences remains the primary bottleneck of transcriptome analysis. The transcript is the sum of the RNA molecules of an organism. Transcriptome analysis is an important first step in functional annotation, which serves as an important clue for the selection of genome editing targets.

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Because the genomes of some insects are larger than the human genome, the arduous process of whole-genome sequencing is even more complicated. So scientists are using transcriptome sequencing along with next-generation sequencing technology, also known as RNA sequencing, as a tool for evaluating large genome-sized insects. With this powerful tool, scientists can efficiently identify tens of thousands of potential genes in a specific tissue by collecting tens of millions of reads. They then assemble the gene sequences into transcriptional units for identification. But this type of analysis is dependent on scientists having access to comprehensive datasets and their functional annotations. Databases exist, but they are unable to keep pace with the increase in insect genome sequencing.

As transcriptome analysis becomes more popular, many research groups are running their own pipelines, providing information about transcription units from various 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 functional annotations from all the different groups doing this type of research into public databases.

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

The Fanflow4Insects workflow for Bugs is developed openly on GitHub, and is freely accessible. In conjunction with functional annotation derived from expression, the data from Fanflow4Insects can be applied to comparative studies of insects with different phenotypes. “Using Fanflow4Insects, we are going to annotate insects that produce useful substances. The ultimate goal of this study is to make it possible to design molecular networks in insects using computer simulations,” Bono said.

The research team included Hidemasa Bono, Hiroshima University; Takuma Sakamoto and Hiroko Tabunoki, Tokyo University of Agriculture and Technology; and Takeya Kasukawa, RIKEN Center for Integrative Medical Sciences.

This research was funded by a Japan Society for the Promotion of Science Kakenhei grant, an open innovation platform for industry-education co-creation (COI-Next), the Japan Science and Technology Agency, and ROIS-DS-Joint.

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