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- Title
The genomic ecosystem of transposable elements in maize.
- Authors
Stitzer, Michelle C.; Anderson, Sarah N.; Springer, Nathan M.; Ross-Ibarra, Jeffrey
- Abstract
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity. Author summary: Transposable elements (TEs) are pieces of DNA that can jump to new positions in the genome. When they land at a new location, they generate a mutation. Such mutations in genes affecting kernel and plant pigmentation allowed the discovery of TEs in maize in the 1940's. Since, we have learned that TEs are a ubiquitous feature of eukaryotic genomes, and that TEs make up over 85% of all the DNA in a maize genome. Here, we investigate the roles of individual TE copies and TE species interacting within the maize genome, and how these relationships are analogous to ecological communities. The community of transposable elements within a single genome represents a rich diversity of ecological strategies for survival in the complex, hostile environment of a host genome.
- Subjects
NON-coding DNA; EUKARYOTIC genomes; BIOTIC communities; PLANT DNA; GENETIC variation; CORN
- Publication
PLoS Genetics, 2021, Vol 17, Issue 10, p1
- ISSN
1553-7390
- Publication type
Article
- DOI
10.1371/journal.pgen.1009768