Detection of sex chromosomes in Tephritid pests using R‐CQ and KAMY, two computational methods to support generic pest management applications

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The detection and characterization of sex chromosome sequences is particularly important for major pest families, like the Tephritidae, whereas alternative pest management approaches, mainly involving male-only release programs, rely on the ability to target and manipulate sex-specific genomic regions, particularly those of the Y chromosome. However, resolving and detecting X and Y chromosome sequences at the chromosome level requires careful consideration of algorithmic outputs, especially in species where extensive sex chromosome markers are not available. Here, we present R-CQ and KAMY, two computational methods developed for the detection of sex chromosome-linked sequences through sex-specific short-read DNA sequencing datasets. We evaluate their performance on newly generated chromosome-level assemblies of four important Tephritid pest species: Ceratitis capitata, Bactrocera dorsalis, Bactrocera zonata, and Anastrepha ludens. By combining algorithmic predictions with a manual curation process, we assess the strengths and limitations of each method and provide a robust dataset of curated X- and Y-linked sequences. Overall, our results establish a framework for studying poorly characterized sex chromosome lineages and identifying sex-specific genomic regions, supporting the broader development of sex chromosome-based pest managements systems.

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