Raimondeau, P. orcid.org/0000-0002-1005-2926, Bianconi, M.E. orcid.org/0000-0002-1585-5947, Pereira, L. orcid.org/0000-0001-5184-8587 et al. (3 more authors) (2023) Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage. New Phytologist, 240 (5). pp. 2072-2084. ISSN 0028-646X
Abstract
Summary Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics.
We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses.
We detect 168 laterally acquired genes in the five reference genomes (32–100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6–28 per Ma) and subsequent losses (11–24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02–0.8% per Ma).
This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2023 New Phytologist Foundation. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. https://creativecommons.org/licenses/by/4.0/ |
Keywords: | Poaceae; adaptation; evolution; horizontal gene transfer; phylogenomics |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 09 Oct 2023 15:59 |
Last Modified: | 04 Oct 2024 15:42 |
Status: | Published |
Publisher: | Wiley |
Refereed: | Yes |
Identification Number: | 10.1111/nph.19272 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:204080 |