Publication:

Transposable elements in basidiomycete fungi: dynamics and impact on genome architecture and transcriptional profiles

Transposable elements (TE), also known as mobile elements or transposons, are enigmatic genetic units that have played important roles in the evolution of eukaryotes. Their impact on genome architecture and phenotypic traits has been widely studied in plants and animals, ever since their discovery in maize during the 1950s by Barbara McClintock. Their ability to move from one locus to another makes them natural tools for generating diversity, as this characteristic leads to genomic alterations with deleterious, neutral, or beneficial effects on hosts. Thus, their survival in the genome depends on the equilibrium between their own benefit and their host’s “permissibility.” Plant and animal TEs have received much attention, yet very little is known about their occurrence and impact on the fungal kingdom. In fact, the first fungal TE was described in Neurospora crassa in 1989, about 40 years later than the discovery of the first TE in plants. Today, revolutionary advances in genome sequencing have opened the possibility of studying non-model species at a whole-genome level. The number of fungal-sequenced genomes increases daily at an unprecedented rate, and most efforts are being concentrated on basidiomycetes, a group of fungi of great interest due to their role in natural ecosystems and their use in multiple industrial applications. In this sense, the amount of genomic information released offers a unique opportunity to start deciphering the effect that mobile, repetitive elements have on fungal genomes. At the time of the start of this PhD thesis (January 2013), very little information regarding basidiomycete TEs existed, as most research was focused on the functional characterization of protein-coding genes. In light of these precedents, the main topics covered in this work are the distribution, characteristics, and impact of transposons in fungal genomes, with an emphasis on basidiomycetes. Using Pleurotus ostreatus as a working model, bioinformatics pipelines have been developed to dig into the extensive genomic data to obtain high quality TE annotations. This approach has allowed for the quantification and characterization of the transposon load of many fungal species and for the testing of hypotheses about the effect that TE insertions produce at the genomic and transcriptomic level.