Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

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.

Chromosome‐level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

“…The seven largest scaffolds are all characterized by high gene density towards both telomeres and a high density of repeats and TEs in the pericentromeric and centromeric regions (Figure 1 , Figure S1 ). While the protein‐coding gene fraction of the genome is similar in size to other closely related Brassicaceae (Wang et al ., 2011 ), the large repetitive fraction suggests an increased genome size driven by TE expansion (Beric et al ., 2021 ). In addition, the spatial distribution of sRNA loci followed the gene density but was concentrated predominantly at the boundary between genes and TEs.…”

New Insights Into the Evolution of C4 Photosynthesis Offered by the Tarenaya Cluster of Cleomaceae

“…Considering the correlation between the 2C value and the 2n chromosome number of Tarenaya species and G. gynandra , we hypothesize that euploidy and disploidy (ascendant and/or descendant) resulted in interspecific variations in the 2C value and C 4 photosynthetic mechanism of G. gynandra . Alternatively, genome size differences may be attributable to whole genome duplications ( Mabry et al, 2020 ) and/or changes in repetitive DNA content ( Beric et al, 2020 , 2021 ).…”

Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales)

“…Using low‐coverage sequencing data from 71 Brassicales taxa, Beric et al. (2021) confirmed that repeat content, along with the gene content and tandem repeats, is an important contributor to genome size variation in the order. In Brassicaceae and Cleomaceae, TEs account for 21% of the Arabidopsis genome (Quesneville, 2020) and 43% of Spider Flower ( Cleome hassleriana ) genome (Cheng et al., 2013) (Figure 5).…”

“…The simplified plastome‐based tree showing phylogenetic relationships among selected Brassicales genomes was adapted from Figure 1a. Red bars correspond to repetitive fractions (%) of the nuclear genomes (data source: Arabidopsis thaliana , Wang et al., 2021 ; Carica papaya , Ming et al., 2008; Moringa oleifera , Tian et al., 2015; Tarenaya hassleriana , Cheng et al., 2013; repeatome proportions in the remaining genomes were estimated by RepeatExplorer using low‐coverage sequence data from Li et al., 2021, Beric et al., 2021 and this study). Genome size and chromosome number of S. caeruleus are unknown.…”

“…In contrast, tandem repeats did not amplify and/or were purged (Figure 2a). Since no significant shifts in TE abundance were associated with WGDs in Brassicales (Beric et al., 2021), genome obesity in Limnanthaceae is likely due to the proliferation of TEs rather than the At‐β genome duplication. Recombination‐based processes are known to remove repeats from the genome (Novák et al., 2020).…”