Scientists expand entomology research using genome editing

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

Researchers have developed a workflow method, called Fanflow4Insects, which describes the function of genes in insects. In functional annotations, scientists collect information about the biological identity of genes. The team’s new method uses transcribed sequence information as well as genome and protein sequence databases. With Fanflow4Insects, the team has annotated functional information of Japanese stick insects and silkworms, including gene expression and sequence analysis. The functional annotation information provided by their workflow will greatly expand the possibilities of entomological research using genome editing.

The team, with scientists from Hiroshima University, Tokyo University of Agriculture and Technology, and the RIKEN Center for Integrative Medicine, published their Fanflow4Insects method on June 27 in the journal Insect.

Insects are so diverse and abundant that scientists need a way to study them on a large scale. This is what prompted scientists to start working on sequencing the insect genome. By May 2022, scientists had cracked the code and registered the genomes of about 3000 insect species. They also used long-read sequencing technology to further accelerate the pace of sequencing the insect genome.

Next-generation sequencing has made it easier for researchers to decode the genomes of many insects along with their transcript sequences. However, the biological interpretation of these sequences remains a major obstacle to transcriptome analysis. The transcriptome is the number of RNA molecules of an organism. Transcriptome analysis is an important first step in functional annotation, serving as an important clue for selecting genome editing targets.

Since some insects have genomes that are 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 evaluate large-genome insects. With this powerful tool, scientists can efficiently identify tens of thousands of possible genes in a given tissue by collecting tens of millions of reads. They then assemble the gene sequence into a transcriptional unit for identification. But this type of analysis relies on scientists having access to comprehensive data sets and their functional annotations. Databases do exist, but they cannot keep pace with the increase in sequencing of insect genomes.

As transcriptome analysis became more popular, many research groups ran their own channels, with information on the transcriptional units of various studies reported on a study-by-study basis. This pipeline is a collection 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 a public database.

In the current study, the research team used the newly developed Fanflow4Insects to create functional annotation channels for silkworms. Then the researchers also tested Fanflow4Insects for the Japanese stick insect transcriptome. “Functional annotation is one of the most important processes to accelerate the selection of target genes after the genome or transcriptome of the target organism has been translated. The functional annotation information obtained by the Fanflow4Insects workflow will greatly expand the possibilities of entomological research using genome editing,” said Hidemasa Bono, a professor in the Graduate School of Integrated Science for Life at Hiroshima University, and first and related author on the paper. .

The Fanflow4Insects workflow for insects has been developed openly on GitHub, and is freely accessible. With respect to expression-derived functional annotations, data from Fanflow4Insects can be applied to comparative studies of insects with different phenotypes. “Using Fanflow4Insects, we will annotate insects that produce beneficial substances. The ultimate goal of this research is to make it possible to design molecular networks in insects using computer simulations,” said Bono.

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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 Medicine.

This research was funded by the Japan Society for the Promotion of Science Kakenhi grant, an open innovation platform for industry-academic co-creation (COI-NEXT), Japan Science and Technology Agency, and ROIS-DS-JOINT.

About Hiroshima University

Since its founding in 1949, Hiroshima University has strived to be one of the most prominent and comprehensive universities in Japan for the promotion and development of scholarship and education. Consisting of 12 undergraduate schools and 4 graduate schools, ranging from natural sciences to humanities and social sciences, the university has developed into one of Japan’s leading comprehensive research universities.
English website: https://www.hiroshima-u.ac.jp/en

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