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High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in

J R L Depotter1, B Ökmen1, M K Ebert1

  • 1CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany.

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|August 16, 2022
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Summary
This summary is machine-generated.

Transposable elements (TEs) drove genome expansion in barley smut (Ustilago hordei) through increased long terminal repeat retrotransposons (LTR-RTs). This proliferation is linked to accelerated gene evolution and a unique substitution pattern.

Keywords:
DNA polymeraseUstilagogenome expansionmating typemating-type locustransposable element

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Area of Science:

  • Genomics
  • Molecular Evolution
  • Fungal Genetics

Background:

  • Transposable elements (TEs) are key drivers of eukaryotic genome diversity.
  • The barley smut fungus, Ustilago hordei, exhibits recent genome expansion.
  • Long terminal repeat retrotransposons (LTR-RTs) are major contributors to genome size variation.

Purpose of the Study:

  • To investigate the role of TEs in the genome expansion of Ustilago hordei.
  • To analyze the correlation between LTR-RTs, mating-type locus size, and nucleotide substitution patterns.
  • To understand the impact of TE proliferation on gene evolution, particularly secretome genes.

Main Methods:

  • Genome assembly of 6 Ustilago hordei strains and 3 related species using long-read sequencing.
  • Quantification of LTR-RT fractions and assessment of their correlation with genome size and mating-type locus.
  • Analysis of nucleotide substitution rates and patterns in TE-rich regions and their proximity to genes.

Main Results:

  • Larger genome sizes in Ustilago hordei are primarily due to increased LTR-RT fractions.
  • LTR-RT fractions positively correlate with mating-type locus size, reaching up to ~560 kb.
  • TE proliferation is associated with elevated nucleotide substitution rates, including a higher fraction of CG substitutions, accelerating secretome gene evolution.

Conclusions:

  • Recent LTR-RT proliferation significantly contributes to the genome expansion of Ustilago hordei.
  • This TE proliferation induces a distinct nucleotide substitution regime, impacting gene evolution.
  • TEs may influence DNA polymerase error rates, driving observed evolutionary patterns.