Molecular evolution of imprinted, orphan and De novo genes in plant genomes
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A range of different genetic processes can facilitate species-specific adaptations. These include orphan genes and genes subject to genomic imprinting. All organisms are known to contain unique genes that have no recognizable homolog in other lineages. These genes are known as orphan genes. Genomic imprinting refers to a phenomenon independent of Mendelian genetics where only one allele is actively expressed depending on its parent of origin. Both processes have been argued to play key roles in plant evolution but their molecular and evolutionary biology is poorly characterized, largely due to the fact that both orphan genes and imprinted genes have only been identified from a handful of model plant species. In this thesis, I have identified orphan genes in the genomes of two crop species, Camelina sativa and Sorghum bicolor. Camelina sativa is an oilseed crop of the Brassicaceae family, whereas Sorghum bicolor is the fifth most important cereal crop belonging to the Poaceae family. Orphan genes identified in these two important crops are important sets of genes that may have played a role in acquiring adaptation to different environmental conditions and other unique characteristics to these species. In addition, a set of novel chimeric open reading frames (ORFs) is identified in Cajanus cajan which is another important food crop. The cytoplasmic male sterility (CMS) trait in plants is often associated with chimeric ORFs that are the products of mitochondrial genome rearrangements and can cause pollen abortion. The novel chimeric ORFs identified represent the most promising candidates for CMS-related mitochondrial rearrangements in Cajanus cajan. Therefore, my research on newly originated genes in agronomically important crops not only has meaningful evolutionary implications for the fundamental biology of species but can also assist plant breeding. To further understand the evolution of plant imprinted genes and critically assess theories concerning their evolution and origins, I assessed the level of positive selection in orthologs of known Arabidopsis thaliana imprinted genes. Orthologs of imprinted genes were extracted from an orthology database developed in this Thesis from 34 sequenced Viridiplantae species. The results suggested a significant elevated level of Arabidopsis thaliana-specific positive selection in Arabidopsis thaliana imprinted paternally expressed genes (iPEGs). Most of the positively selected sites identified in imprinted genes showed fixation in Arabidopsis thaliana population data. As positive selection may drive the fixation of beneficial traits within a population, imprinted genes that showed fixation of positively selected sites are the best candidates for further functional studies. Genomic imprinting in plants is identified to be mainly restricted to the seed endosperm. Genome-wide allele-specific expression analysis conducted in this thesis using a F1 triploid hybrid system demonstrates that altering the genome dosage can induce genomic imprinting in plant tissues (in embryos) where imprinting does not occur at the diploid level.
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