Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae)

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.

The ecology of palm genomes: repeat‐associated genome size expansion is constrained by aridity

“…We found that the amount of the genome occupied by certain repeat lineages correlated significantly with genome size variation in palms. This suggests that the preferential expansion of particular repeat lineages drives genome size diversity in palms, as shown in other plant groups (Macas et al ., 2015; Pellicer et al ., 2021). Moreover, our results suggest that total repeat genome proportion changed asymptotically with genome size, indicating shifts in repeat ‘community’ composition and turnover across the range of palm genome sizes.…”

Genome Insights into Autopolyploid Evolution: A Case Study in Senecio doronicum (Asteraceae) from the Southern Alps

“…Comparison of the proportion of different types of repetitive elements was carried out by plotting pairwise scatterplots comparing the number of shared reads of each DNA repeat class between the different cytotypes as in Pellicer et al [55], where the slope of the plot represents the genome size ratio between cytotypes. Linear regressions were performed using the lm function in R and differences between genome compositions were checked by performing a permanova test using the adonis function in the vegan package in R.…”

Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View

“…The proliferation of tandem repeats has a much smaller impact on the variation in genome size when compared with retrotransposons [ 43 ]. The highly amplified satellite families contributed significantly to the increase in genome size in Heloniopsis umbellata [ 55 ], Fritillaria affinis [ 29 ] and Oenothera biennis [ 56 ].…”