Biology subjects

Benson, C. W.

Publications and source records attributed to Benson, C. W..

2 recordsLinked to original sources

bioRxiv2025

TESS: A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction

Genome expansion and contraction are reportedly driven by transposable element (TE) activity, but the underlying dynamics remain enigmatic due to a lack of historical records tracing these changes. Here, we present PrinTE for versatile, forward-time simulation of whole-genome sequences with highly customizable transposon dynamics. Through simulations, we confirm that the distribution of TE sequence divergence reflects their historical insertion and deletion dynamics, which can be used to infer TE dynamic parameters through PrinTE simulations. We analyzed the pangenome of Pucciniomycotina, a subdivision of fungi containing myrtle rust (Austropuccinia psidii), which drastically expanded its genome size to 1018 Mb. Our analyses reveal that the best strategy for controlling genome size is to avoid the invasion of LTR retrotransposons (LTR-RTs). While illegitimate recombination (IR) is considered the most effective counteraction of LTR-RT invasions leaving only solo LTR remnants, we observed a strong positive correlation between solo:intact LTR ratio (strength of LTR-RT removal) and genome size (r = 0.65), and a near-linear correlation between solo LTR count and genome size (r = 0.98). This result suggests that IR alone may not effectively prevent genome obesity. Through simulation of Pucciniomycotina genomes, we proposed that A. psidii might experience a prolonged period of genome expansion followed by a short, potent, and likely ongoing period of contraction. PrinTE is freely available at https://github.com/cwb14/PrinTE.git.

bioinformatics↗

bioRxiv2023

The genome of Salmacisia buchloëana, the parasitic puppetmaster pulling strings of sexual phenotypic monstrosities in buffalograss

To complete its parasitic lifecycle, Salmacisia buchloeana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloeanas ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloeana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloeana is nested within the genus Tilletia and diverged from T. caries and T. walkeri [~]40 million years ago. We find that S. buchloeana has a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloeanas evolution and host specificity. Salmacisia buchloeana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation and that S. buchloeana has a unique bias for the serine codon UCG. Finally, we identify three inteins within the S. buchloeana genome, two of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.

genomics↗