Alexandros Bousios

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis

This study identifies centromeric repeat turnovers in Arabidopsis species, revealing evolutionary mechanisms and the role of genetic drift and centromere drive in repeat replacement.

Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana

This study identifies 200,000 new transposable element insertions in Arabidopsis thaliana, revealing integration biases and adaptive potential of somatic transposition.

ATHILAfinder: a tool to detect ATHILA LTR retrotransposons in plant genomes

ATHILAfinder detects ATHILA LTR retrotransposons in plant genomes with high accuracy, outperforming existing tools in recovery and precision.

Pangenome analysis reveals the evolutionary dynamics of repeat-based holocentromeres

The paper analyzes Tyba satellite DNA repeats and transposable elements in holocentric species to reveal evolutionary dynamics of repeat-based holocentromeres across a pangenome.

Diverse patterns of secondary structure across genes and transposable elements are associated with siRNA production and epigenetic fate

The paper identifies secondary structure patterns in maize genes and transposable elements linked to siRNA production and epigenetic variation.

The genetic and epigenetic landscape of the Arabidopsis centromeres

Ultra-long-read sequencing resolves Arabidopsis centromeres, revealing their genetic and epigenetic structure and dynamics.

Gene capture by transposable elements leads to epigenetic conflict in maize

The paper investigates epigenetic conflict in maize caused by transposable elements capturing gene fragments, showing that captured genes are more methylated and targeted by siRNAs, while translocated genes show signs of silencing and pseudogenization.

The Genomics of Selfing in Maize (Zea mays ssp. mays): Catching Purging in the Act

The paper investigates purging dynamics in selfed maize lines, finding increased homozygosity and genome size reduction due to purging of deleterious variants and transposable elements.

Considerations and complications of mapping small RNA libraries to transposable elements

The paper examines challenges in mapping small RNA libraries to transposable elements in maize, highlighting methodological considerations and their impact on TE age analysis.