Transcriptomic, small RNA, and epigenetic atlas of the Brassica napus seed

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Ziegler, Dylan
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The diversification of flowering plants has been described as the “abominable mystery” of evolutionary biology for decades. Angiosperms diversified at unprecedented rates in the early Cretaceous, rapidly occupying new niches and pervading much of the earth’s terrestrial landscape. This speciation was accompanied by dramatic genome evolution as well — more than 75% of extant angiosperm species are believed to have originated from genome duplication events. These duplications are most often in the form of endogenous chromosomal duplication (autopolyploidy) or, more frequently, via interspecific hybridization (allopolyploidy). Consequently, dynamics of polyploidy within flowering plants are of interest to the fields of plant genetics and evolution. One of the world’s most important oilseeds is Brassica napus L. (“canola”), an allopolyploid species derived from two progenitors (B. rapa and B. oleracea). B. napus has two relatively complete diploid genomes from each progenitor, but also shares a whole genome triplication (autopolyploidization) with the rest of the Brassicaceae. These factors constitute B. napus as an informative model to study the consequences of polyploidization. Within this thesis, I describe the transcriptional and epigenetic profiles throughout B. napus seed development. Therein, I utilize laser microdissection, histological analysis, and bioinformatic tools to describe the transcriptional profiles of the seed. The subgenomes constituting B. napus contribute to gene expression within the seed asymmetrically, with many homlogs being more expressed in one subgenome than the other. Additionally, I provide evidence for striking differences in epigenetic structure of the fractionated genomes depending on genomic context. The works detailed within this thesis serve to explain the transcriptional landscapes of the B. napus seed, particularly through the lens of polyploidy, and the exceptional complexity of angiosperm genomes.
canola, seed development, epigenetics, brassica, brassica napus, transcriptome