Abstract
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
Highlights
Transposable elements (TEs) are DNA sequences that self-propagate across genomes and are ubiquitous components of almost all prokaryotic [1] and eukaryotic genomes such as plants (e.g., [2,3], fungi [4] and animals [5,6])
In this work we studied the content of transposable elements in the genome of the lichen-forming fungus U. pustulata
We analyzed the variation in TE insertion frequency in populations representing two ecotypes distributed along three gradients spanning the elevational range of the species, i.e., from the Mediterranean to cold temperate climate zones
Summary
Transposable elements (TEs) are DNA sequences that self-propagate across genomes and are ubiquitous components of almost all prokaryotic [1] and eukaryotic genomes such as plants (e.g., [2,3], fungi [4] and animals [5,6]). Most TEs present in eukaryotic genomes are genomic fossils, i.e., inactive remnants of once-active copies [10,11]. Their variation in copy number and size is responsible for much of the large differences in genome size observed even among closely related species [12,13,14]. The most recent, likely active, transposable fraction of the mobilome—all repeated sequences except microsatellites—
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