Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools
- 1HudsonAlpha Institute for Biotechnology
Abstract
A complete reference genome for species with chromosomally-determined separate sexes should contain scaffolds for all sex chromosome homologs. However, sex chromosomes present distinct computational challenges compared to autosomes. Here we present a k-mer based analysis that utilizes whole-genome sequencing of a few sex-identified isolates: Cytogenetics-By-Sequencing (CBS) tools. Unlike other approaches that typically address one aspect of the sex chromosomes, CBS-tools strives to guide users from the discovery of the heterogametic sex through identifying the sex-determination region (SDR). The core of CBS-tools is automated quantification of sex-specific k-mers in order to predict the heterogametic sex. Using publicly-available datasets, CBS-tools correctly identified the known sex-system of the 31 species tested. Additionally, we used these k-mers to verify and correct phasing of sex chromosomes between haplotypes in species representing different sex-systems. Finally, we used these k-mers to delimit the SDR boundary using an interactive web platform. CBS-tools was developed with previously unexplored sex chromosome systems in mind, but is also suitable for well-examined sex chromosome pairs.
Related
- Lens species genome assemblies reveal evolutionarily fragile chromosomes associated with pericentric inversions
- Functionally identified neuronal assemblies robustly encode stimuli and are structurally delineated by inhibition
- Identifying crossovers in a cattle pangenome containing haplotype-resolved assemblies from half-siblings
- Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D
- TabularQual: a spreadsheet-based format for annotating and curating logical models in SBML-qual
BibTeX
@misc{whitt2026identifying,
title = {{Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools}},
author = {L. Whitt and L. Akozbek and P. C. Bentz and E. Armstrong and A. Harkess and S. B. Carey},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.23.753885},
url = {https://www.biorxiv.org/content/10.64898/2026.09.23.753885v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools
AU - L. Whitt
AU - L. Akozbek
AU - P. C. Bentz
AU - E. Armstrong
AU - A. Harkess
AU - S. B. Carey
PY - 2026
DA - 2026/09/23
PB - bioRxiv
DO - 10.64898/2026.09.23.753885
UR - https://www.biorxiv.org/content/10.64898/2026.09.23.753885v1
AB - A complete reference genome for species with chromosomally-determined separate sexes should contain scaffolds for all sex chromosome homologs. However, sex chromosomes present distinct computational challenges compared to autosomes. Here we present a k-mer based analysis that utilizes whole-genome sequencing of a few sex-identified isolates: Cytogenetics-By-Sequencing (CBS) tools. Unlike other approaches that typically address one aspect of the sex chromosomes, CBS-tools strives to guide users from the discovery of the heterogametic sex through identifying the sex-determination region (SDR). The core of CBS-tools is automated quantification of sex-specific k-mers in order to predict the heterogametic sex. Using publicly-available datasets, CBS-tools correctly identified the known sex-system of the 31 species tested. Additionally, we used these k-mers to verify and correct phasing of sex chromosomes between haplotypes in species representing different sex-systems. Finally, we used these k-mers to delimit the SDR boundary using an interactive web platform. CBS-tools was developed with previously unexplored sex chromosome systems in mind, but is also suitable for well-examined sex chromosome pairs.
ER -