CYPiBASE

Pests are responsible for up to 18% annual crop yield losses. In a world of growing agricultural needs, it is very important to reduce their impact using all available tools of integrated pest management. Some herbivorous insects have become especially good at resisting natural and artificial pesticides.

Metazoan organisms have evolved into a three-phase system to help them cope with constant exposure to xenobiotics found in their environment. Xenobiotics are deactivated, metabolized and excreted by different enzymes, and cytochrome P450 (CYP) is the main enzyme involved in the phase I of the detoxification system. CYPs represent a superfamily of monooxygenases hemoproteins found in all kingdoms, and their largest diversification among eukaryotes is mainly observed in insects.
Recent surveys estimate that approximately 27% of predicted P450s in public databases are incorrect due to partial sequences, chimeric assemblies, or misassigned paralogs. These inaccuracies are exacerbated by automated genome annotation pipelines, which often perform poorly when genes occur in clusters—a common feature of P450 families.

The CYPiBASE project is a database with a unique manually curated CYP dataset, containing more than 2000 CYP genes from agronomically important insects (pests or parasitoids) (Gouin et al, 2017; Chertemps et al, 2021). An additional 3000 proteins sequences from 31 complete insect P450s will also be used in our project (Dermauw et al, 2020). All our genes are named and classified in families based on their amino acid sequence similarities with the official curated names.

CYPiBASE will centralise:

• curated gene and protein sequences mapped to specific genome assemblies,
• mutated CYP variants found in field populations and associated with resistance or susceptibility to pesticides,
• promoter and regulatory regions, enabling identification of motifs involved in gene-expression control.

The second part of the project is to develop an improved annotation pipeline for future genomes. Cytochrome P450 gene curation is time consuming and there is more and more insect genomes release. This improved annotation approach may incorporate machine learning or other artificial intelligence–based methods. This improvement in CYP annotation is crucial for the IPIE team to maintain its high level of expertise in insect detoxification as the number of available insect pest genomes is blooming.