| dc.description.abstract |
Transposable elements (TEs) are a heterogeneous collection of DNA sequences characterised by their ability to relocate to new sites of the genome, employing either a cut-and-paste mechanism or an RNA intermediate. As a result, TEs are able to quickly replicate through the genome to such a degree that, often, they constitute the majority of the genome in plant species. Their replicative activity is usually harmful for their host genomes, thus, TEs tend to be considered genomic parasites and their activity is constantly suppressed by the host genome. In plants, TE silencing is achieved via a combination of the three epigenetic marks that maintain genome stability. One of such marks, small RNAs (sRNAs), consist of single stranded RNA molecules ranging from 20 to 24 nucleotides in size generated from a longer double stranded precursor. These sRNAs guide the epigenetic machinery to a particular region of the genome using a combination of DNA methylation and histone modifications that change the chromatin conformation of the region, modifying its expression. Hence, vast parts of the plant genome are epigenetically silenced, leading to important phenotypic consequences. Despite this, reference genomes are often generated with a comprehensive annotation of protein coding genes and the mRNAs they produce, but this offers only a partial view of genome functions, many of which involve epigenetic mechanisms.
In this thesis, we generated a new reference genome for the emerging oilseed crop Thlaspi arvense (field pennycress) with a special focus on the de novo annotation of TEs and small RNA loci (sRNA). We annotated 423,249 individual TEs, which together constitute 61% of the T. arvense genome, most of it were long terminal retrotransposons (LTR). To understand how TE activity is regulated, we complemented our TE annotation with sRNA data. Applying a custom pipeline to data from leaf, root, inflorescence and pollen, we identified 19,288 distinct sRNA loci, of which 72 were microRNAs. Then, I examined the dynamics of TE variation in a geographically diverse sample of this species. By surveying almost 300 wild accessions ranging from America to Eurasia, I discovered over 90,000 polymorphic TE insertions and ten times more TE deletions.
In parallel, I also conducted a de novo TE annotation of a set of Arabidopsis thaliana genomes to investigate to what extent TE activity shapes the plant repertoire of a set of disease resistance genes, Nucleotide-binding site leucine-rich repeat (NLR) genes. Comparing NLR loci with their genomic background, I showed that these NLR loci contained a higher proportion of young LTR TEs and a higher proportion of solo LTRs> Comparisons of these NLR loci between accessions also revealed the high prevalence of intraspecific TE variability at these loci. Altogether, this work contributes to the understanding of the nature of the genomic processes that generate the necessary NLR diversity needed to survive in a constantly changing, pathogen-loaded environment. |
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