Genome-wide identification and expression profiling of glycosidases, lipases, and proteases from invasive asian palm weevil, Rhynchophorus ferrugineus

Harith-Fadzilah, Nazmi (author), Nihad, Mohammad (author), AlSaleh, Mohammed Ali (author), Bazeyad, Abdulqader Yaslam (author), Pandurangan, Subash-Babu (author), Munawar, Kashif (author), Vidyawan, Arya (author), Alharbi, Hatten A. (author), Jakše, Jernej (author), Pain, Arnab (author), Antony, Binu (author)

The red palm weevil, Rhynchophorus ferrugineus, is a destructive, invasive pest to a diverse range of palm plantations globally. Commonly used broad-range chemical insecticides for insect control pose high risks to non-target organisms, humans, and the environment. A bio-rational approach of screening natural small-molecule inhibitors that specifically target R. ferrugineus proteins critical to its life processes can pave the way for developing novel bioinsecticides. Digestive enzymes (DEs), which impair feeding on plants (herbivory), are promising targets. We generated de novo transcriptomes, annotated DE-related genes from the R. ferrugineus gut and abdomen, manually annotated the DE gene family from the recently available genome and our transcriptome data, and reported 34 glycosidases, 85 lipases, and 201 proteases. We identified several tandem duplicates and allelic variants from the lipase and protease families, notably, 10 RferLip and 21 RferPro alleles, which emerged primarily through indels and single-site substitution. These alleles may confer enhanced digestive lipolysis and proteolysis. Phylogenetic analyses identified and classified different subfamilies of DEs and revealed close evolutionary relationships with other coleopterans. We assessed select candidate DEs’ activity and the potential for inhibition in silico to better understand the herbivory arsenal. In silico analysis revealed that the selected enzymes exhibited similar ligand-binding affinity to their corresponding substrate, except for protease aminopeptidase N, RferPro40, which exhibited poorer affinity to the inhibitor bestatin. Overall, our study serves as a foundation for further functional analysis and offers a novel target for the development of a novel bio-rational insecticide for R. ferrugineus.

• Language: English
• Keywords: red palm weevil, Rhynchophorus ferrugineus, herbivory, digestive enzyme, gene duplication, phylogeny, molecular docking
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: 27 str.
• Numbering: Vol. 16, iss. 4, art. 421
• PID: 20.500.12556/RUL-168620
• UDC: 60
• ISSN on article: 2075-4450
• DOI: 10.3390/insects16040421
• COBISS.SI-ID: 233303043
• Publication date in RUL: 18.04.2025

Record is a part of a journal

• Title: Insects
• Publisher: MDPI
• ISSN: 2075-4450
• COBISS.SI-ID: 519122457

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: palmov rilčkar, Rhynchophorus ferrugineus, škodljivci rastlin, prebavni encimi, podvajanje genov, filogenija, molekularna genetika

Projects

• Funder: Other - Other funder or multiple funders
• Funding programme: Ministry of Education in Saudi Arabia
• Project number: IFKSUDR_F142