ACE

ACE detects resistance-associated mutations in acetylcholinesterase (Ace) genes from RNA-Seq data to identify target-site variants conferring resistance to organophosphate (OP) and carbamate insecticides.

Key Features:

• Mutation Detection: Identifies known Ace gene mutations associated with insecticide resistance by analyzing RNA-Seq datasets.
• Comprehensive Reference Database: Uses a curated database of known Ace resistance mutations as a reference for variant detection.
• Alignment and Annotation: Aligns sequences against reference genomes and annotates Ace gene regions to locate potential variants.
• Mutation Frequency Calculation: Computes frequencies of resistance-associated mutations within each RNA-Seq dataset to quantify prevalence.
• Large-Scale Data Analysis Capability: Has been applied to 971 RNA-Seq datasets from 136 studies across seven insect pest species and processes next-generation sequencing data at scale.

Scientific Applications:

• Resistance Monitoring and Management: Provides quantitative mutation-frequency data to inform monitoring of target-site resistance in pest populations.
• Population Studies (Anopheles, Uganda): Revealed high frequencies (30%–44%) of resistance-associated Ace mutations in Anopheles datasets from Uganda.
• Cross-Species Analysis (Plutella xylostella): Identified correlations between specific mutations such as G227A and resistance levels to OP or carbamate insecticides in Plutella xylostella.
• Comparative Resistance Assessment: Enabled comparisons across species, documenting low resistance frequency in Nasonia vitripennis versus high frequencies in agricultural pests such as Chilo suppressalis and Bemisia tabaci, where all Ace reads indicated resistance.

Methodology:

Accepts RNA-Seq datasets, aligns reads to reference genomes, annotates Ace gene regions, detects mutations using a curated Ace resistance mutation database, calculates mutation frequencies per dataset, and outputs reports of mutation frequencies.