Investigating mechanisms of rDNA-driven rapid genome evolution using long-read assemblies

Monday, November 11, 2024

11:18 AM – 11:30 AM MST

Location: Phoenix Convention Center, 223, PCC

Presenting Author(s)

RS

Rachel Seamons

Brigham Young University
Provo, Utah

Co-Author(s)

JS

John Sproul (he/him/his)

Brigham Young University
Provo, Utah
Paul Bryan Frandsen

Assistant Professor
Brigham Young University
Provo, Utah
MT

Madeline Tanner

Brigham Young University
Provo, Utah

Tandem arrays of satellite DNAs (satDNAs) are among the most rapidly evolving sequences in genomes. Their expansion, contraction, and movement can play key roles in chromatin regulation, shifts in gene expression, and the process of speciation, and yet the finer details of mechanisms underlying their rapid evolution remain poorly understood. We identified several cases of rapid satDNA evolution in which ribosomal DNA (rDNA) serves as the source sequence of novel satellite repeats. We investigated these patterns using long-read (PacBio HiFi) assemblies of two ground beetle species (Bembidion lividulum and Bembidion testatum). In these closely-related species, rDNA-derived satellite sequences alone account for at least 18% of the difference in overall genome composition. We show evidence that R-elements, retrotransposons which target 28S rDNA, play important roles in the initial formation of rDNA-derived satDNAs in both species. We find that proliferation of these newly formed satDNAs may be driven by both the movement of R-elements within the genome and by the incorporation of the newly formed satDNAs into existing satDNA arrays. We present models for both general and specific molecular mechanisms which may be driving these patterns of rDNA-derived satellite mobilization and proliferation. Further testing of these models may help explain frequent observation of 28S rDNA fragments in unexpected chromosomal locations as reported in cytogenetic literature. This work also highlights how multi-tiered interactions among repetitive sequences ubiquitous in eukaryotes (i.e., rDNA, non-LTR retrotransposons, and satDNA) can drive rapid shifts in repeat architecture on short evolutionary time scales.