Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.09.23.753885

Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools

Whitt, L.·Akozbek, L.·Bentz, P. C.·Armstrong, E.·Harkess, A.·Carey, S. B.
View original source ↗Export metadata ↓

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.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Whitt, L., Akozbek, L., Bentz, P. C., Armstrong, E., Harkess, A., Carey, S. B.. 2026-09-29. Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools. https://doi.org/10.64898/2026.09.23.753885

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Genomic correlates of metastatic competence and progression in human melanoma

Genomic events and their timing that grant a primary tumour the competence to disseminate remain poorly defined. We performed sequencing of 247 stage I/II primary cutaneous melanomas (CMs) and 60 matched metastases without intervening therapy from a prospectively followed registry cohort with a median followup of 92 months, integrating copy-number, mutational, protein and spatial-transcriptomic analyses. Relapse was not distinguished by oncogenic point mutations, which were largely shared between primaries and metastases, but by somatic copy-number alterations (SCNAs) and global chromosomal instability. We defined OncoCycle, a six-gene copy-number signature (amplification of CDK4, MCL1 and CD276; biallelic loss of CDKN2A, CDKN2B and TP53BP1) that predicted relapse independently of established clinicopathological features in melanoma, and a pan-cancer analysis. In matched pairs, metastatic progression was driven by continued copy-number evolution and reduction in intra-tumoural heterogeneity, rather than by acquired point mutations, and OncoCycle alterations from primary tumours were preserved in metastasis seeding clones. Clonal reconstruction revealed both monoclonal and polyclonal metastasis seeding, and spatial transcriptomics resolved copy-number-defined metastatic subclones occupying and programming distinct immune and stromal niches. Thus, metastatic competence was primed early by focal SCNAs on a background of chromosomal instability, elaborated by continued copy-number evolution during dissemination and spatio-temporal interactions with the tumour-microenvironment.

genomics↗
bioRxiv2026

Evolutionary dynamics of the insertion sequence IS6110 in the Mycobacterium tuberculosis complex

Insertion sequences (IS) are the most common type of transposable element in prokaryotes and shape the structure of genomes through transposition and by providing a substrate for recombination. Despite the mutational impact of IS, the evolutionary dynamics of most elements in host species remain unknown. Here we study the dynamics of IS6110 in 10,000 strains of the Mycobacterium tuberculosis complex (MTBC). We developed a tool that allows the detection and comparison of IS insertions from short reads without using a reference genome. Using ancestral state reconstruction (ASR) on presence-absence patterns of IS6110, we describe the distribution of copy numbers (CNs) in the MTBC, infer birth rates of the element, and identify genomic regions with large numbers of parallel IS6110 insertions. Copy numbers in the MTBC range from 1 in some clades to more than 30 in strains of La3 (M. orygis). IS6110 birth rates scale approximately linearly with copy number and are elevated on terminal branches, consistent with the delayed action of purifying selection. A key characteristic of IS6110 is its occurrence in hotspots: the 5% most frequently targeted regions account for half of all independent insertion events. The motif 5'-TCTCAAAW-3' is enriched around target sites and in hotspots, suggesting that the accumulation of insertions in these regions results through a combination of non-random insertion and purifying selection in other regions. To conclude the study, we propose a niche constraints model according to which the distribution of IS6110 in the MTBC is governed by the rarity of regions that have both suitable DNA properties and little functional value for the host.

genomics↗
bioRxiv2026

Alcohol Use Disorder and Smoking-Associated Molecular Alterations in Human Prefrontal Cortex in Single Nucleus (sn) RNA-Seq

Chronic smoking worsens alcohol related brain injury and impairs neurocognitive recovery, yet the cell type specific molecular interactions between alcohol use disorder (AUD) and smoking in the human brain remain largely unexplored. We analyzed single-nucleus RNA-seq from the prefrontal cortex of 73 individuals (614,932 nuclei, 24 cell types), comparing AUD versus controls, smoking versus controls, and combined AUD+smoking versus controls. In excitatory neurons, neuroinflammatory, complement, GPCR, kinase, proteostatic, and extracellular-matrix pathways confined to one or two subtypes in either condition alone expanded across nearly all subtypes when AUD and smoking co-occurred. Inhibitory neurons showed a parallel but distinct expansion, additionally recruiting translational regulation, RNA splicing, and deubiquitination pathways. Smoking alone produced widespread repression of bioenergetic, proteostatic, and synaptic pathways in excitatory neurons, whereas AUD produced mixed pathway activation and repression in excitatory neurons and broad inflammatory activation in inhibitory neurons. In the combined condition, microglia exhibited paradoxical repression of phagocytosis, TYROBP signaling, and translational machinery, consistent with an exhaustion like state, accompanied by an apparently compensatory shift in inflammatory signaling toward astrocytes, oligodendrocyte precursor cells, and oligodendrocytes, which showed coordinated inflammatory activation. Vascular cells showed an endothelial-VLMC dichotomy, with endothelial repression of RNA processing and proteostasis contrasting with perivascular activation. Our analysis identifies bioenergetic and proteostatic stress as the predominant signature of smoking, whereas immune and metabolic activation characterize AUD. In AUD+Smoking, these alterations extend across more neuronal subtypes and include neuroinflammation, complement activation, altered signaling, proteostatic stress, and post-transcriptional remodeling associated with greater cortical dysfunction in co-occurring AUD and smoking.

genomics↗