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In recent years, understanding the emergence and integration of novel genes into genomes has garnered significant interest within the scientific community. Species-specific orphan genes have become particularly intriguing due to their recent appearance and distinct structural characteristics. Despite their prevalence and potential evolutionary significance, studying orphan genes poses challenges due to their lack of similarity to other genes, resulting in limited functional annotations. This study aims to delve into the mechanisms, functions, networks, and agricultural implications of orphan genes. QQS (Qua-Quine Starch), exclusively identified in Arabidopsis thaliana, stands as the first functionally characterized orphan gene in plants. It regulates carbon and nitrogen allocation, influencing traits such as protein levels, starch content, and resistance to pests and pathogens through its interaction with NF-YC4 (Nuclear Factor Y subunit C4). However, the precise mechanism underlying QQS's function, whether as a noncoding transcript, a coding protein, or both—and its network and functional partners remain elusive. Furthermore, it raises questions about the operation of such an orphan gene, lacking homologs in other species, within those species. This study manipulates the QQS gene's sequence to produce exclusive mRNA or protein, unveiling its dual functionality in influencing metabolic pathways. Additionally, the research extends to evaluating the agricultural impact of QQS beyond Arabidopsis, in tobacco and potato. Expressing QQS or overexpressing NF-YC4 in tobacco enhances protein content, reduces starch levels, and strengthens resistance to pests, while in potatoes, it elevates protein content in tubers without affecting yield. Furthermore, exploring QQS's interactions with other orphan or taxonomically-restricted genes like TRQA1 reveals their roles in regulating starch and protein levels, broadening our understanding of plant metabolic regulation through orphan and taxonomically restricted genes. This comprehensive investigation sheds light on orphan gene functionality, highlighting their dual coding and noncoding roles, function through conserved factors across plant species, functional partners and interactors, and potential for crop improvement. These findings hold significance for agricultural sustainability, offering insights into enhancing crop productivity, nutritional quality, and resilience to environmental stresses, thereby addressing global food security challenges.

Plant pathogens have the ability to quickly overcome host resistance and shift to novel hosts. The (re)emergence of plant pathogens is a major concern in agriculture and in conservation of natural landscapes. The rapid adaptation to hosts and new environments depends on the genetic variability in pathogen populations. Despite of the importance of sugarcane for Brazilian agribusiness and the persistence of the smut pathogen Sporisorium scitamineum in most cropping areas, genetic variation studies are still missing for Brazilian isolates. In the chapters 1 and 2, molecular variability studies were performed for Brazilian and Argentine isolates of S. scitamineum, using molecular markers (AFLP, telRFLP) and sequencing (ITS and a candidate effector gene) strategies. No variation was found in ITS sequences. On the contrary, telRFLP marker generates almost a unique fingerprint for each strain. Two genetically distinct groups were formed by the joint analysis of the AFLP and telRFLP markers. The two groups were the same formed by haplotypes of a candidate effector gene. The presence of polymorphisms that causes non-synonymous mutations in a candidate effector gene potentially involved in the specific interaction with sugarcane may cause distinct performances on host genotypes. S. scitamineum is part of the highly diverse clade of Ustilaginomycetes fungi that includes several smut disease agents. Despite being phylogenetically close and present similar lifestyles, species of smut fungi have distinct and narrow host ranges. Hence, another objective in this thesis was to identify the genetic basis of host specialization in smut fungi using comparative genomics analyses. In chapter 3, the mating-type loci were described in S. scitamineum genome and compared among smut fungi. Transposable elements are the likely mechanism causing chromosomal rearrangements between mating-type loci. The presence of trans-specific polymorphisms at the genes encoding pheromone/receptor proteins suggests a hybridization potential among smut species. In the chapter 4, a broad comparative genomics analysis was performed among nine species of smut fungi infecting distinct hosts. The genetic basis of host specialization in smut fungi is complex and seems to involve a range of evolutionary processes, including gene gain/loss and episodic selection events. Species-specific effectors and positively selected genes will be good candidates for further characterization in regards to their role in host adaptation. / Fitopatógenos apresentam a habilidade de rapidamente suplantar os mecanismos de defesas da planta e adaptar-se a um novo hospedeiro. A (re)emergência de patógenos é uma das maiores preocupações na agricultura e na conservação de populações naturais. A rápida adaptação ao hospedeiro e a novos ambientes depende da variabilidade genética nas populações de patógenos. Apesar da importância da cana-de-açúcar para o agronegócio brasileiro e da persistência do patógeno Sporisorium scitamineum, o agente causal do carvão da cana-de-açúcar, na maioria das áreas canavieiras, estudos de variabilidade genética ainda não foram realizados para isolados brasileiros. Nos capítulos 1 e 2, estudos de variabilidade molecular foram realizados para isolados brasileiros e argentinos de S. scitamineum, usando marcadores moleculares (AFLP e telRFLP) e dados de sequenciamento (ITS e um gene candidato a efetor). Nenhum polimorfismo foi encontrado usando sequências ITS. Contrariamente, o marcador telRFLP gerou quase um fingerprint para cada linhagem. Dois grupos geneticamente distintos foram formados pela análise conjunta dos marcadores telRFLP e AFLP. Os dois grupos também foram formados pelos haplótipos obtidos pelo sequenciamento de um candidato a efetor. A presença de polimorfismos causando mutações não-sinônimas em um candidato a efetor pode acarretar em performances distintas em diferentes genótipos de cana-de-açúcar. S. scitamineum pertence à classe Ustilaginomycetes, a qual também abrange vários outros agentes causais de doenças do carvão. Apesar de filogeneticamente próximos e com estilo de vida similar, espécies de carvão apresentam uma faixa distinta e estreita de hospedeiros. Portanto, outro objetivo desta tese foi identificar a base genética da especialização ao hospedeiro por fungos causadores de carvão usando análises de genômica comparativa. No capítulo 3, os loci envolvidos na determinação do tipo de reação sexual (mating-type) foram caracterizados no genoma de S. scitamineum e comparados com sequências de outras espécies de carvão. Tranposons foram identificados como provável mecanismo de rearranjo cromossômico entre os loci de mating-type. Polimorfismos trans-específicos nos genes codificadores de feromônios e receptores sugerem o potencial de hibridização entre espécies de carvão. No capítulo 4, análises de genômica comparativa abrangendo nove espécies de carvão infectando hospedeiros distintos foram realizadas. A base genética da especialização ao hospedeiro em fungos causadores de carvão é complexa e parece envolver processos evolutivos de ganho/perda de genes e seleção positiva. Efetores espécie-específicos e sob seleção positiva são destacados como bons candidatos para serem caracterizados quanto ao papel que estabelecem na adaptação ao hospedeiro.