Which factors contribute most to genome size variation within angiosperms?

Abstract

Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It has been reported that many factors correlate with the variation in genome size, but few studies have systematically explored this at the genomic level. Here, we scan genomic information for 74 species from 74 families in 38 orders covering the major groups of angiosperms (the taxonomic information was acquired from the latest Angiosperm Phylogeny Group (APG IV) system) to evaluate the correlation between genome size variation and different genome characteristics: polyploidization, different types of repeat sequence content, and the dynamics of long terminal repeat retrotransposons (LTRs). Surprisingly, we found that polyploidization shows no significant correlation with genome size, while LTR content demonstrates a significantly positive correlation. This may be due to genome instability after polyploidization, and since LTRs occupy most of the genome content, it may directly result in most of the genome variation. We found that the LTR insertion time is significantly negatively correlated with genome size, which may reflect the competition between insertion and deletion of LTRs in each genome, and that the old insertions are usually easy to recognize and eliminate. We also noticed that most of the LTR burst occurred within the last 3 million years, a timeframe consistent with the violent climate fluctuations in the Pleistocene. Our findings enhance our understanding of genome size evolution within angiosperms, and our methods offer immediate implications for corresponding research in other datasets.

Keywords: angiosperm; genome size; long terminal repeat; polyploidization; repeat sequences.

Figure 1

The distributions of plant genome sizes (a) and mean LTR insertion times (b). The density curves represent the distribution, while the scatter diagram and the box‐plot show the statistics including median, quartile and the outliers

Figure 2

Representation of phylogeny and the correlation factors analyzed in 74 genomes. GF: genome size fold, PF: polyploidization fold, tandem: tandem repeats, and LTR insertion dates. GF indicates the genome size fold in plants scaled by the ancestral genome size for angiosperms and PF indicates the value of polyploidization fold which is the number of times that whole‐genome duplication and the whole‐genome triplication occurred. LTR‐tandem indicates different proportions of corresponding repeating elements in genomes as a percentage (%). Mean insertion date indicates the estimated distribution of LTR insertion dates in plants in millions of years. The WGDs and WGTs are labeled in the branches. The topology information cited is from Li et al. (2019)

Figure 3

Different factors (in colors) as a function of genome size. Different factors fitted against genome size fold (genome size scaled by ancestral genome size for angiosperms). The gray lines represent the estimated result from phylogenetic least squares (PGLS) analysis. (a‐f) The relationship between the proportion of different repeated elements against genome size fold in 74 species. (g) The absence of a relationship between polyploidization fold and genome size fold. (h) The mean date of LTR insertions was significantly correlated with genome size fold. Lines are plots of linear regressions