Digital Kennison: a bioinformatics pipeline for rapid mapping of sequences to the Drosophila melanogaster Y chromosome
Abstract
The Drosophila melanogaster Y chromosome is currently known to contain 13 single-copy protein-coding genes, 6 of which are essential for male fertility, as well as several noncoding genes and abundant repetitive DNA. Localization of Y-linked sequences has traditionally relied on labor-intensive crosses using Kennison's translocation strains, which map Y-linked loci by generating flies deficient for each of the 6 Y chromosome fertility regions (ks-1, ks-2, kl-1, kl-2, kl-3, and kl-5). Here, we present Digital Kennison, a computational pipeline that recasts this classical mapping strategy as a sequence-based analysis. The pipeline queries 8 genomic databases derived from Kennison's strains using BLAST and read coverage, assigning sequences to fertility regions or the centromeric region with a calibrated confidence score. We benchmarked the method on 60 Y-linked sequences spanning all 7 regions, including single-copy protein-coding genes, Mst77Y family members, noncoding RNAs, and the centromere. Digital Kennison achieved 97% precision while resolving challenging cases, including boundary-spanning genes (PRY and Ppr-Y), fragmented Mst77Y copies, and FDY, which has a closely related autosomal paralog. Beyond validating known localizations, the pipeline localized the unmapped gene CG41561 to the kl-1region and reassigned the transcript CR40629-RC from the kl-2 region to kl-5. It also localized 7 of 16 recently transferred Y-linked sequences, including 4 with high confidence. Applied to 904 R6 scaffolds, Digital Kennison assigned 75% to fertility regions, including 5 currently annotated as autosomal-pericentromeric. Digital Kennison reduces sequence localization from weeks of genetic crosses to minutes of computation while preserving the power of classical translocation mapping.
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BibTeX
@article{uno2026digital,
title = {{Digital Kennison: a bioinformatics pipeline for rapid mapping of sequences to the Drosophila melanogaster Y chromosome}},
author = {Fabiana Uno and A Bernardo Carvalho},
journal = {G3: Genes | Genomes | Genetics},
year = {2026},
month = sep,
doi = {10.1093/g3journal/jkag253},
url = {https://doi.org/10.1093/g3journal/jkag253},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Digital Kennison: a bioinformatics pipeline for rapid mapping of sequences to the Drosophila melanogaster Y chromosome
AU - Fabiana Uno
AU - A Bernardo Carvalho
PY - 2026
DA - 2026/09/10
JO - G3: Genes | Genomes | Genetics
DO - 10.1093/g3journal/jkag253
UR - https://doi.org/10.1093/g3journal/jkag253
AB - The Drosophila melanogaster Y chromosome is currently known to contain 13 single-copy protein-coding genes, 6 of which are essential for male fertility, as well as several noncoding genes and abundant repetitive DNA. Localization of Y-linked sequences has traditionally relied on labor-intensive crosses using Kennison's translocation strains, which map Y-linked loci by generating flies deficient for each of the 6 Y chromosome fertility regions (ks-1, ks-2, kl-1, kl-2, kl-3, and kl-5). Here, we present Digital Kennison, a computational pipeline that recasts this classical mapping strategy as a sequence-based analysis. The pipeline queries 8 genomic databases derived from Kennison's strains using BLAST and read coverage, assigning sequences to fertility regions or the centromeric region with a calibrated confidence score. We benchmarked the method on 60 Y-linked sequences spanning all 7 regions, including single-copy protein-coding genes, Mst77Y family members, noncoding RNAs, and the centromere. Digital Kennison achieved 97% precision while resolving challenging cases, including boundary-spanning genes (PRY and Ppr-Y), fragmented Mst77Y copies, and FDY, which has a closely related autosomal paralog. Beyond validating known localizations, the pipeline localized the unmapped gene CG41561 to the kl-1region and reassigned the transcript CR40629-RC from the kl-2 region to kl-5. It also localized 7 of 16 recently transferred Y-linked sequences, including 4 with high confidence. Applied to 904 R6 scaffolds, Digital Kennison assigned 75% to fertility regions, including 5 currently annotated as autosomal-pericentromeric. Digital Kennison reduces sequence localization from weeks of genetic crosses to minutes of computation while preserving the power of classical translocation mapping.
SN - 2160-1836
ER -