No abstract

Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

Genome size of plants has long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana -chosen as the model plant system for this reason -as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we find no correlation between genome size and TE content, and more surprisingly we identify no significant changes to TE landscape following WGD. . Paul Blischak from the University of Arizona, and Christian Concepcion for their assistance in both getting software to run and help in understanding models, and code development. We thank our Molecular and Network Evolution course at the University of Missouri, which enabled our project and introduced the co-first authors to one another. We thank both our funding and computational resources; Department of Energy Defense Threat Reduction Agency (HDTRA 1-16-1-0048), National Science Foundation (IOS 1339156), and the Research Computing Support Services (RCSS) at the University of Missouri. Lastly, we thank our anonymous reviews for their comments and edits of our manuscript. AUTHOR CONTRIBUTIONSAB, MEM, AEH, PPE, MES, GCC, BCM, and JCP designed the study. MEM grew, sampled, and collected RNA/DNA from plants. AB conducted TE annotation, regression analyses and phylogenetic comparisons of TE-derived phylogeny to species tree. MEM performed species tree inference and comparative genomic analyses. AEH and GCC helped with analyses. AB and MEM wrote the manuscript. All authors provided feedback and helped shape the final manuscript. LITERATURE CITEDÅgren, J. A., H. R. Huang, and S. I. Wright, 2016 Transposable element evolution in the allotetraploid Capsella bursa-pastoris. Am. J. Bot. 103:1197-1202.

[EMBARGOED UNTIL 6/1/2023] In Chapter 1, I examined the relationship between TEs and genome size in the Brassicales, in Chapter 2 I characterized sRNAs in Brassicaceae, and in Chapter 3 I evaluate nat-siRNAs as a sRNA type. In this introduction, I provide background on the diversity of angiosperms, with special focus on the Brassicales order, plant genomes, and small RNAs and their biogenesis.

We model the post-hexaploidy evolution of four genomes from the Solanaceae, a group of flowering plants comprising tomatoes, potatoes and their relatives. The hexaploidy that these genomes descend from occurred through two sequential allopolyploidy events and was marked by the unequal losses of duplicated genes from the different progenitor subgenomes. In contrast with the hexaploid Brassiceae (broccoli and its relatives), where the subgenome with the most surviving genes arrived last in the hexaploidy, among the Solanaceae the most preserved subgenome descends from one of the original two tetraploid progenitors. In fact, the last-arriving subgenome in these plants actually has the fewest surviving genes in the modern genomes. We explore whether the distribution of repetitive elements (REs) in these genomes can explain the biases in gene losses, but while the signals we find are broadly consistent with a role for high RE density in driving gene losses, the REs turn over so quickly that little signal of the RE condition at the time of paleopolyploidy is extant in the modern genomes.