Abstract
Plant genomes vary greatly in composition and size mainly due to the diversity of repetitive DNAs and the inherent propensity for their amplification and removal from the host genome. Most studies addressing repeatome dynamics focus on model organisms, whereas few provide comprehensive investigations across the genomes of related taxa. Herein, we analyze the evolution of repeats of the 13 species in Melampodium sect. Melampodium, representing all but two of its diploid taxa, in a phylogenetic context. The investigated genomes range in size from 0.49 to 2.27 pg/1C (ca. 4.5-fold variation), despite having the same base chromosome number (x = 10) and very strong phylogenetic affinities. Phylogenetic analysis performed in BEAST and ancestral genome size reconstruction revealed mixed patterns of genome size increases and decreases across the group. High-throughput genome skimming and the RepeatExplorer pipeline were utilized to determine the repeat families responsible for the differences in observed genome sizes. Patterns of repeat evolution were found to be highly correlated with phylogenetic position, namely taxonomic series circumscription. Major differences found were in the abundances of the SIRE (Ty1-copia), Athila (Ty3-gypsy), and CACTA (DNA transposon) lineages. Additionally, several satellite DNA families were found to be highly group-specific, although their overall contribution to genome size variation was relatively small. Evolutionary changes in repetitive DNA composition and genome size were complex, with independent patterns of genome up- and downsizing throughout the evolution of the analyzed diploids. A model-based analysis of genome size and repetitive DNA composition revealed evidence for strong phylogenetic signal and differential evolutionary rates of major lineages of repeats in the diploid genomes.
Highlights
Nuclear genome size is a strikingly variable characteristic of the flowering plants
We extend the aforementioned results to test hypotheses that (1) genome size evolution has included both up- and downsizing, (2) repetitive DNA composition of these diploid genomes is strongly correlated with the phylogeny of the section, and (3) repeat lineages have different rates of evolution
The clades representing the different series in section Melampodium had very high support (97–100%)
Summary
Nuclear genome size is a strikingly variable characteristic of the flowering plants. Current estimates show more than 2000-fold genome size variation from the smallest known genomes of the carnivorous Genlisea (Lentibulariaceae; ca. 0.06 pg/1C) to the largest of Paris japonica (Melanthiaceae, 152.2 pg/1C) (Pellicer et al, 2010; Fleischmann et al, 2014). Frequently occurring in plants, results in instant multiplication of the whole nuclear genome, differential evolution of the repetitive component of the genome explains the majority of the observed genome size variation in angiosperms (Bennetzen, 2005). Repetitive DNA in plant genomes consists of two broad categories of repeat types, the dispersed mobile elements and tandem repeats (Bennetzen and Wang, 2014). The long-terminal-repeat (LTR) retrotransposons are the most frequently occurring elements in most plant genomes and are typically distributed throughout the chromosomes. These repeats encompass several superfamilies, of which Ty1-copia and Ty3-gypsy are the most common in plants (Wicker et al, 2007). Which of these two superfamilies predominates in the genome can differ between plant groups/families (Novák et al, 2014; Kelly et al, 2015; Macas et al, 2015)
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