Alyazeedi, T. | Search bioRxiv

bioRxiv2025

PanScan: A Tool for Tertiary Analysis of Human Pangenome Graphs

The genomic representation of populations across the globe is critical to ensuring a comprehensive and equitable human reference. Constructing a pangenome graph reference for different populations is the best approach to addressing local genomic diversities. Although major initiatives across continents are underway to construct pangenome graph references, the field lacks the necessary toolsets for tertiary analysis to characterize telomere-to-telomere (T2T) assemblies and the complexity of haplotypes. PanScan is a bioinformatics software package developed for human pangenome tertiary analysis. It includes multiple modules designed to detect duplicated gene sets from T2T assemblies, identify novel variants and sequences, as well as detect and visualize complex genomic regions through pangenome graph haplotype loops. We have used multiple pangenomes across different populations to assess the tertiary analysis and their accuracy. The tool is designed to streamline tertiary analysis and is compatible with multiple pangenome graph construction algorithms. PanScan is freely available on GitHub (https://github.com/CATG-Github/panscan), where users can provide human pangenome assemblies or VCF files as inputs for automated analyses through command-line operations on Linux systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/651685v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@16cc212org.highwire.dtl.DTLVardef@13961d0org.highwire.dtl.DTLVardef@44d194org.highwire.dtl.DTLVardef@1b72aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

The X chromosome is a potential polarising signal for asymmetric cell divisions in meiotic cells of a nematode

The unequal partition of molecules and organelles during cell division results in daughter cells with different fates. Asymmetric cell divisions have been best characterised in systems in which extrinsic signals polarise the mother cell during cell division. However, the mechanisms of asymmetric cell division mediated by intrinsic signals, and the nature of these signals, are mostly unknown. Here we report an asymmetric cell division in the nematode Auanema rhodensis that may be cued by the X chromosome. In the wildtype XO male, the spermatocyte divides asymmetrically to generate X-bearing spermatids that inherit components necessary for sperm viability, and nullo-spermatids that inherits components to be discarded. We found that in XX mutant pseudomales, sperm components co-segregate with the X chromosome, supporting the hypothesis that the X chromosome is employed as a polarising signal for partitioning essential cytoplasmic components for sperm function.

developmental biology↗