About

Worldwide, pests account for a 5-20% loss of crop yield, and this is estimated to increase to 10-25% due to a warming climate [1]. The availability of pest insect genomes is playing an increasingly important role in crop protection research. Taking the Securing Productivity Programme at Rothamsted as an example, genomes have played a major role in our work and in the work of collaborators.

Some examples are:

• Understanding insecticide resistance: Genomes allow access to the sequences of the target site proteins (e.g. [2]) for identifying mutations that cause resistance and elucidating how insecticides interact with the proteins (e.g. [3])

• Designing more selective chemistry: By comparing sequences of target site proteins in different species (e.g. [4])

• Understanding selectivity of insecticides: Sequences of detoxification enzymes show which insecticides are toxic to non-target insects and which are unlikely to cause damage (e.g. for neonicotinoids and bees [5] [6])

• Identifying the basis of insect evolution: Genome data can identify how some insects can adapt to feed on new host plants and hence become a potential new pest threat (e.g. [7])

• Identifying and understanding odorant binding proteins: These are involved in host and mate location and identifying them may lead to novel control by blocking the insect’s reactions to these cues. (e.g.[8])

• Developing gene editing techniques for Drosophila and crop pests: these are very valuable for testing gene function, for example resistance mutations and fitness costs (e.g. [9])

These areas are under study by many other groups in the UK and around the world. The challenge for genomics researchers in the sustainable agriculture research community is that the number of high-quality pest and beneficial insect genomes available is very limited. Of the 555 insect species with sequences in NCBI (12/11/2020) only 61 can be considered as high quality (with assemblies to chromosome level). Only 14 of these are crop pests and just 1 being relevant to UK crops. This situation is what motivated our industry partners to propose the Pest Genomics Initiative (PGI). They were frustrated that their researchers working on pesticide mode of action and insecticide resistance programmes did not have pest genomes with sufficient assembly quality and accurate gene annotations needed for their discovery research programmes.

Thus, a pre-competitive project between three partners, Rothamsted, Bayer, and Syngenta to sequence and assemble high quality genomes for 20 insect agricultural pests of world-wide importance was established. We aimed to complete the genomes to chromosome level and have accompanying gene annotations with curated models from the P450, UGT, ABC, and IRAC set of genes to ensure research ready resources and that they are freely available upon completion of the project.

Objectives:

• Assemble and annotate 20 insect pest species of agricultural importance to high quality.

• Curation of genes of interest that often occur in tandem duplications and are poorly annotated: P450, UGT, ABC.

• Curation of IRAC genes - 26 main groups of insecticides/acaricides (excl. microbial disruptors of midgut function).

• Submit all data to the public upon project end date.

References:

1. Deutsch, C.A., et al.,Science, 2018. 361(6405): p. 916-919

DOI: 10.1126/science.aat3466.

2. Dale, R.P., et al.,Insect Mol Biol, 2010. 19 Suppl 2: p. 141-53

DOI: 10.1111/j.1365-2583.2009.00975.x.

3. O'Reilly, A.O., et al.,Pest Manag Sci, 2014. 70(3): p. 369-77

DOI: 10.1002/ps.3561.

4. Amey, J.S., et al.,FEBS Letters, 2015. 589(5): p. 598-607

DOI: https://doi.org/10.1016/j.febslet.2015.01.020.

5. Manjon, C., et al.,Curr Biol, 2018. 28(7): p. 1137-1143 e5

DOI: 10.1016/j.cub.2018.02.045.

6. Beadle, K., et al.,PLoS Genet, 2019. 15(2): p. e1007903

DOI: 10.1371/journal.pgen.1007903.

7. Bass, C., et al.,Proc Natl Acad Sci U S A, 2013. 110(48): p. 19460-5

DOI: 10.1073/pnas.1314122110.

8. Vieira, F.G., et al.,PLoS One, 2012. 7(8): p. e43034

DOI: 10.1371/journal.pone.0043034.

9. Homem, R.A., et al.,Mol Ecol, 2020. 29(14): p. 2661-2675

DOI: 10.1111/mec.15503.