Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae

• Published in: G3 : genes - genomes - genetics Vol. 10; no. 12; pp. 4387 - 4398
• Main Authors: Ramachandran, Dhanushya, McKain, Michael R, Kellogg, Elizabeth A, Hawkins, Jennifer S
• Format: Journal Article
• Language: English
• Published: England Genetics Society of America 01-12-2020; Oxford University Press
• Subjects: adaptation; copia insertions; Investigations; ltr retrotransposon; maize domestication; tripsacum dactyloides; adaptation; Tripsacum dactyloides; maize domestication; LTR retrotransposon; copia insertions
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1534/g3.120.401596

Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the
clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various
and
species, in addition to two closely related diploid species,
and
, revealed variation in repeat content among all taxa included in the study. The repeat composition of
is more similar to that of
and
compared to
, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the
superfamily, specifically in
and
, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically,
insertions in
and
were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post
divergence. The lack of
insertions near the orthologous genes in
suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.