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

The detection and characterization of sex chromosome sequences is particu-larly important for major pest families, like the Tephritidae, whereas alternative pest man-agement approaches, mainly involving male-only release programs, rely on the ability totarget and manipulate sex-specific genomic regions, particularly those of the Y chromo-some. However, resolving and detecting X and Y chromosome sequences at the chro-mosome level requires careful consideration of algorithmic outputs, especially in specieswhere extensive sex chromosome markers are not available. Here, we present R-CQ andKAMY, two computational methods developed for the detection of sex chromosome-linked sequences through sex-specific short-read DNA sequencing datasets. We evalu-ate their performance on newly generated chromosome-level assemblies of four impor-tant Tephritid pest species: Ceratitis capitata, Bactrocera dorsalis, Bactrocera zonata, andAnastrepha 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 cu-rated X- and Y-linked sequences. Overall, our results establish a framework for studyingpoorly characterized sex chromosome lineages and identifying sex-specific genomic re-gions, supporting the broader development of sex chromosome-based pest managementssystems.