The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

Jack S. Gisby, Marco Catoni

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Abstract

Pack-TYPE transposable elements (TEs) are a group of non-autonomous DNA transposons found in plants. These elements can efficiently capture and shuffle coding DNA across the host genome, accelerating the evolution of genes. Despite their relevance for plant genome plasticity, the detection and study of Pack-TYPE TEs are challenging due to the high similarity these elements have with genes. Here, we produced an automated annotation pipeline designed to study Pack-TYPE elements and used it to successfully annotate and analyse more than 10,000 new Pack-TYPE TEs in the rice and maize genomes. Our analysis indicates that Pack-TYPE TEs are an abundant and heterogeneous group of elements. We found that these elements are associated with all main superfamilies of Class II DNA transposons in plants and likely share a similar mechanism to capture new chromosomal DNA sequences. Furthermore, we report examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack-TYPE TEs in plant genome evolution.
Original languageEnglish
Article numbere1010078
Number of pages19
JournalPLoS Genetics
Volume18
Issue number2
DOIs
Publication statusPublished - 24 Feb 2022

Bibliographical note

Funding Information:
MC work is partially funded by the Royal Society Research Grant [RGS\R1\201297] (https:// royalsociety.org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Part of the computations described in this paper were performed using the University of Birmingham?s Compute and Storage for Life Sciences (CaStLeS) service.

Publisher Copyright:
Copyright: © 2022 Gisby, Catoni. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Keywords

  • genomics
  • Research and analysis methods
  • Engineering and technology
  • Biology and life sciences
  • Research Article

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