Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae
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 shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and...
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| Format: | Article |
| Language: | English |
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Oxford University Press
2020-12-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.120.401596 |
| _version_ | 1818618099535970304 |
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| author | Dhanushya Ramachandran Michael R. McKain Elizabeth A. Kellogg Jennifer S. Hawkins |
| author_facet | Dhanushya Ramachandran Michael R. McKain Elizabeth A. Kellogg Jennifer S. Hawkins |
| author_sort | Dhanushya Ramachandran |
| collection | DOAJ |
| description | 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 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 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 LTR-retrotransposons were abundant in all species, 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 retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. 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. |
| first_indexed | 2024-12-16T17:16:12Z |
| format | Article |
| id | doaj.art-8e65aa8ccc02454dac43d1c820e25d60 |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-16T17:16:12Z |
| publishDate | 2020-12-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-8e65aa8ccc02454dac43d1c820e25d602022-12-21T22:23:17ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362020-12-0110124387439810.1534/g3.120.40159610Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe AndropogoneaeDhanushya RamachandranMichael R. McKainElizabeth A. KelloggJennifer S. HawkinsBoth 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 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 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 LTR-retrotransposons were abundant in all species, 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 retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. 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.http://g3journal.org/lookup/doi/10.1534/g3.120.401596adaptationltr retrotransposoncopia insertionsmaize domesticationtripsacum dactyloides |
| spellingShingle | Dhanushya Ramachandran Michael R. McKain Elizabeth A. Kellogg Jennifer S. Hawkins Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae G3: Genes, Genomes, Genetics adaptation ltr retrotransposon copia insertions maize domestication tripsacum dactyloides |
| title | Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae |
| title_full | Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae |
| title_fullStr | Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae |
| title_full_unstemmed | Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae |
| title_short | Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae |
| title_sort | evolutionary dynamics of transposable elements following a shared polyploidization event in the tribe andropogoneae |
| topic | adaptation ltr retrotransposon copia insertions maize domestication tripsacum dactyloides |
| url | http://g3journal.org/lookup/doi/10.1534/g3.120.401596 |
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