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

PLoS Genet. 2022 Feb 24;18(2):e1010078. doi: 10.1371/journal.pgen.1010078. eCollection 2022 Feb.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Transposable Elements* / genetics
  • Evolution, Molecular
  • Genome, Plant / genetics
  • Oryza* / genetics
  • Zea mays / genetics

Substances

  • DNA Transposable Elements

Grants and funding

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.