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.
Highlights
Gymnosperms today comprise a little more than 1000 species that are two to three orders of magnitude lower than c. 352,000 species of extant angiosperms [1]
These discoveries highlight that transposable elements (TEs) and epigenetic components tightly interact through numerous pathways and suggest their joint implication in organisms’ responses to stress
A three-fold increase in the genome size of diploid members of Gossypium is due to the accumulation of long-terminal repeat retrotransposons (LTR-RTs) over the past 5–10 mya [122]
Summary
Gymnosperms today comprise a little more than 1000 species that are two to three orders of magnitude lower than c. 352,000 species of extant angiosperms [1]. Morphologically recognizable fossil angiosperms first appeared more recently In the ancient and widespread plant lineages of gymnosperms, two-thirds are conifers (Coniferales or Pinophyta), mainly including Pinaceae and Cupressophytes of 546–615 species [7,8]. This lineage plays an important role in global carbon, nutrient, and atmospheric cycles and is of great ecological and economic importance worldwide. Recent years have witnessed fascinating strides in our understanding of the genome evolution and adaptation in conifer species, owing to next-generation sequencing technologies and interdisciplinary developments, Genes 2019, 10, 228; doi:10.3390/genes10030228 www.mdpi.com/journal/genes. We review some of the most updated examples on the roles of transposable elements (TEs) in plant genome evolution and adaptation through epigenetics mechanisms, whereby we discuss how TEs and ncRNAs (and DNA methylation) dynamics contribute to conifer genomic and adaptive evolution
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