Transposable elements in basidiomycete fungi: dynamics and impact on genome architecture and transcriptional profiles
Fecha
2017Autor
Director
Versión
Acceso abierto / Sarbide irekia
Tipo
Tesis doctoral / Doktoretza tesia
Impacto
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nodoi-noplumx
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Resumen
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 ...
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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. [--]
Materias
Elementos transponibles (ETs),
Transposable elements (TE),
Molecular analysis,
Análisis molecular
Departamento
Universidad Pública de Navarra. Departamento de Producción Agraria /
Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila
Programa de doctorado
Entidades Financiadoras
This work has been supported by Spanish National Research Plan and U.S. Department of Energy: Effect of helitrons in genome structure and transcriptional profile of Pleurotus ostreatus (AGL2011-30495). Study of the interactions between transcriptome and methylome to explain differences in growth rate and mushroom yield in the edible fungus Pleurotus ostreatus (AGL2014-55971-R). Joint Genome Institute and Office of Science of the U.S. Department of Energy under Contract No (DE-AC02-05CH11231).