Biology subjects

Sweeten, A. P.

Publications and source records attributed to Sweeten, A. P..

3 recordsLinked to original sources

bioRxiv2026

AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates

MotivationSatellite DNA has long posed challenges for genome assembly and analysis due to its low sequence complexity and poor mappability. These large heterochromatic arrays of tandem repeats are ubiquitous across eukaryotic genomes, yet remain understudied. Current methods for annotating satellite regions, and other classes of tandem repeat arrays, are limited in their ability to annotate divergent or novel sequences. ResultsIn this work, we introduce AniAnns, an algorithm for annotating large blocks of tandemly repeating DNAs. AniAnns exploits the high Average Nucleotide Identity (ANI) shared between repeat units of the same array to quickly and accurately infer the boundaries of such arrays. We show that AniAnns improves the annotation of satellites and other tandem repeats within a variety of plant and animal genomes, while requiring only a fraction of the runtime compared to previous approaches. We conclude by exploring several use cases of AniAnns as a lightweight method for masking repeats prior to whole-genome alignment as well as the de novo annotation and classification of satellite repeats. AvailabilityAniAnns is open source software and available at github.com/marbl/anianns

bioinformatics↗

bioRxiv2025

Origin and evolution of acrocentric chromosomes in human and great apes

The short arms of human acrocentric chromosomes are characterized by nucleolar organizer regions essential for ribosome biogenesis, but their highly repetitive nature has hindered genomic analysis. Leveraging the recently completed genomes of all major ape lineages, we identified recurrent features of their acrocentrics, including enriched repeat classes, centromere repositioning by whole-arm inversion, interchromosomal sequence exchange, and birth-and-death evolution of multiple gene families. Together, these processes have enabled the repeated amplification and diversification of the FRG1 gene family over 25 million years of ape evolution, and, in gorilla, the formation and amplification of a novel IGSF3-GGT fusion gene under positive selection. Similar evolutionary events also explain the distribution of segmental duplications and heterochromatin in the modern human genome, predisposing it to karyotypic abnormalities such as Robertsonian translocations. Our findings highlight acrocentric chromosomes as key drivers of evolution in the great apes, with implications for speciation, adaptation, and clinical genomics.

genomics↗

bioRxiv2024

ModDotPlot - Rapid and interactive visualization of complex repeats

MotivationA common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy. ResultsIn this work we introduce ModDotPlot, an interactive and alignment-free dot plot viewer. By approximating average nucleotide identity via a k-mer-based containment index, ModDotPlot produces accurate plots orders of magnitude faster than StainedGlass. We accomplish this through the use of a hierarchical modimizer scheme that can visualize the full 128 Mbp genome of Arabidopsis thaliana in under 5 minutes on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes. Availability and ImplementationModDotPlot is available at https://github.com/marbl/ModDotPlot. Contactalex.sweeten@nih.gov, adam.phillippy@nih.gov

bioinformatics↗