Evolutionary dynamics of transposable elements following a shared polyploidization event in the tribe Andropogoneae

Abstract

Word count: 5718Abstract Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a recent shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed existing variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although the genomes of all species studied had abundant LTR-retrotransposons, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these copia elements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. The lack of copia insertions near the orthologous genes in S. bicolor 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.

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

“…Andropogoneae species include maize, sorghum, sugarcane, and silvergrass, some of the most productive grain, sugar, and biofuel crops worldwide (Manners 2011;Brosse et al 2012). Andropogoneae species share the NADP-ME C 4 photosynthesis system (Black et al 1969;Sage and Zhu 2011) and similar development patterns, whereas their genomes are highly diverse with frequent polyploidization (Estep et al 2014) and extremely active transposable elements (TEs) (Ramachandran et al 2020). Nevertheless, despite rapid sequence turnover elsewhere in Andropogoneae genomes, functional sequences are expected to be under purifying selection, making the tribe an ideal system in which to identify and understand the role of CNSs.…”

HEMU: an integrated Andropogoneae comparative genomics database and analysis platform

“…As a predominant structural element of Andropogoneae genomes, Researchers studied TE (transposable element) insertions across the whole genome in a maize diversity panel and discovered that TE insertional polymorphisms were tagged by SNP markers associating with agricultural trait (Qiu et al, 2021). What's more, it is also investigated that TE-induced phenotypic changes were associated with domestication and/or diversification in Andropogoneae (Ramachandran et al, 2020).…”