Novel Insights into Plant Genome Evolution and Adaptation as Revealed through Transposable Elements and Non-Coding RNAs in Conifers

Abstract

Plant genomes are punctuated by repeated bouts of proliferation of transposable elements (TEs), and these mobile bursts are followed by silencing and decay of most of the newly inserted elements. As such, plant genomes reflect TE-related genome expansion and shrinkage. In general, these genome activities involve two mechanisms: small RNA-mediated epigenetic repression and long-term mutational decay and deletion, that is, genome-purging. Furthermore, the spatial relationships between TE insertions and genes are an important force in shaping gene regulatory networks, their downstream metabolic and physiological outputs, and thus their phenotypes. Such cascading regulations finally set up a fitness differential among individuals. This brief review demonstrates factual evidence that unifies most updated conceptual frameworks covering genome size, architecture, epigenetic reprogramming, and gene expression. It aims to give an overview of the impact that TEs may have on genome and adaptive evolution and to provide novel insights into addressing possible causes and consequences of intimidating genome sizes (20⁻30 Gb) in a taxonomic group, conifers.

Keywords: adaptation; adaptive evolution; conifers; evolutionary genomics; genome purging; non-coding RNAs; transposable elements.

Figure 1

Conceptual illustration of key realizations in plant genome architecture. The merger of two diploids via hybridization and/or allopolyploidy has novel evolutionary consequences [21], enumerated in the black cylinder.

Figure 2

Comparison of genome size, protein-coding transcripts, and transposable elements between conifers and other sequenced tree species. In (A), estimated mean genome sizes of major conifer species is based on the Plant DNA C-values Database (http://data.kew.org/cvalues/) as of February 2019. All botanical illustrations are from the public domain (Note S1). In (B–D), the number of species (n) used in each calculation is different due to incomplete information available in original publications. The p-values based on t-tests are given on the top of each panel. p-values for the comparisons of class I and II TEs between conifers and non-conifer trees were 0.005 and 0.94, respectively. The data used for these plots were extracted from the publications listed in Table S1.