Comparison of RNAi Sequences in Insect-Resistant Plants to Expressed Sequences of a Beneficial Lady Beetle: A Closer Look at Off-Target Considerations

Abstract

Sequences obtained from transcriptomes of the lady beetle Coleomegilla maculata were compared to those designed for incorporation into crops. Searches of the transcriptomes identified sequences as the most likely to be closely similar to the sequences described in RNAi plant incorporated products. Some proposed prime RNAi pest management targets were also used to identify predicted orthologs from C. maculata. The lady beetle sequences were aligned with sequences from corn rootworms and Colorado potato beetles and, as appropriate in the case of targets, regions of similarity were compared with the genetic model organism for beetles, Tribolium castaneum. Some high levels of nucleotide identity were identified, particularly with an actin-derived sequence from Colorado potato beetle. This actin-derived sequence shared identical sequences with the lady beetle and a parasitic wasp.

A Perspective on RNAi-Based Biopesticides

“…Using a database of arthropods and other key species, the software indicates which off-target species have 21nt matches, and allows for the operator to test different regions of a target gene to minimise off-target hits. This application has been used to examine CBP and WCR target genes (b-actin and DvSnf7 respectively) for putative off-target impacts on the lady beetle Coleomegilla macula and the red flour beetle Tribolium castaneum (Allen, 2017). Another common approach to identify off-target hits has been to use the BLAST search tool.…”

Piwi/piRNAs control food intake by promoting neuropeptide F expression in locusts

“…In addition to the use of pesticides, RNAi approaches in which dsRNAs are designed to suppress target genes and then the target gene is processed into an siRNA have been considered as potential strategies for pest management (Kunte et al , 2020 ). However, sufficient nucleotide sequence similarity of the target gene raises the possibility of detrimental cross‐species effect (Jackson et al , 2003 ; Allen, 2017 ). Approximately 79% similarity (15/19) between an siRNA and a target gene with 11 contiguous matched bases is sufficient to trigger the expression silencing of off‐target transcripts.…”

Evaluation of a cuticle protein gene as a potential RNAi target in aphids

“…Thus, a safety assessment of natural enemies, such as predators, during molecular target selection should be made . Genes with high identity (>75%), including actin , were studied in the beneficial insect Coleomegilla maculata , and the pest Leptinotarsa decemlineata suggested that the RNAi used to control Colorado potato beetle should avoid these genes . When treated with the dsRNA of vATPase A from Diabrotica virgifera virgifera , Adalia bipuncata suffered a prolonged developmental time, and Adalia bipuncata had a lower survival rate .…”

“…43,44 Genes with high identity (>75%), including actin, were studied in the beneficial insect Coleomegilla maculata, and the pest Leptinotarsa decemlineata suggested that the RNAi used to control Colorado potato beetle should avoid these genes. 45 When treated with the dsRNA of vATPase A from Diabrotica virgifera virgifera, Adalia bipuncata suffered a prolonged developmental time, and Adalia bipuncata had a lower survival rate. 46 Silencing of a gut protease, cathepsin L, induced 80% mortality of M. persicae but also disrupted the growth of C. septempunctata for reduced protein content.…”