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 p...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 chromosomelinked 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.展开更多
基金supported by the International Atomic Energy Agency research contract no.23378 as part of the Coordinated Research Project“Generic approach for the development of genetic sexing strains for SIT applications.”This research was supported by the European Union’s Horizon Europe Research and Innovation Programme REACT(Grant agreement 101059523)the three postgraduate programs of the Department of Biochemistry and Biotechnology of the University of Thessaly(“Advanced Experimental&Computational Biosciences,”“Biotechnology-Quality Assessment in Nutrition and the Environment”and“Applications of Molecular Biology-Genetics-Diagnostic Biomarkers”).
文摘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 chromosomelinked 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.
