Abstract
Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.
Highlights
Plant genomes are dynamic and can expand in size through a variety of processes such as the proliferation of repetitive elements, and whole genome duplications (Wang D. et al, 2021)
In this work we provide the first insights into genome evolutionary dynamics in the genus Heloniopsis, by combining high throughput sequence data and cytogenetics
Our analysis showed that the most recent common ancestor of Heloniopsis likely had an Ancestral 1C-values (Anc1C) of 3,022 Mb, indicating that during the evolution of H. umbellata its genome has expanded by 1,658 Mb
Summary
Plant genomes are dynamic and can expand in size through a variety of processes such as the proliferation of repetitive elements (including transposable elements and tandem repeats), and whole genome duplications (Wang D. et al, 2021). Melanthiaceae stand out within monocots as being among the most diverse, with genome sizes varying > 230-fold (Pellicer et al, 2014). This is even more remarkable given that this family is made up of just c. The main driver underpinning the extensive genome size diversity in Melanthiaceae lies in a striking genome expansion that occurred during the diversification of tribe Parideae. This event is estimated to have taken place c. This raises the question as to what are the key mechanisms responsible for underpinning such genome size differences among closely related taxa?
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