Variation detection in organelle genomes of Quercus species

• Autor(a) principal: Ferreira, Ana Rita Moreira
• Data de Publicação: 2021
• Tipo de documento: Dissertação
• Idioma: eng
• Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
• Texto Completo: http://hdl.handle.net/10348/10416
• topic: Quercus genus; Organelle genomes

The use of next-generation sequencing (NGS) technologies has been revolutionizing the study of genetics. The big amount of generated data by these technologies allows the characterization of species genomes and genomic variation between species and within the same one. The present dissertation focused on the study of single nucleotide polymorphisms (SNPs) in organelle genomes of two well-known species of Quercus: Quercus suber and Quercus ilex rotundifolia, commonly named cork oak and holm oak respectively. Chloroplasts and mitochondria are organelles present in plant cells and play a crucial role in photosynthesis and energy metabolism, respectively, among other important physiological functions. Each of these organelles has its own genome, distinct from the nuclear genome. Within the Quercus genus, the chloroplast genome sequences have been determined for over 20 species, including cork oak which was assembled by the Genosuber consortium, and only the cork oak mitochondrial genome has been determined to date. Moreover, the amount of information on genomic variation is very scarce in chloroplast genomes, or non-existent in mitochondrial genomes. Therefore, there is a clear need to increase our knowledge in this field, given the importance of these species in the ecosystem and their socio-economic impact especially in the south region of the Iberic Peninsula. The pipeline of this study involves the use of high-throughput sequencing data of 47 individuals (39 cork oaks and 8 holm oaks) using NGS techniques and tools to perform quality control, preprocessing, read mapping, variant calling and annotation. Additionally, to achieve the best performance on preprocessing and variant calling the used tools were tested using different parameters on a smaller group of individuals. As it was expected given the higher conservation of chloroplast genomes, the presented results show a higher variation on mitochondrial genomes, especially when comparing cork oak with holm oak trees. These variations suggest a different capacity in both species and some studies have been reporting that holm oak is more resistant than cork oak and these variations may be the reason for that. With this in mind, it is possible to say that holm oak trees have greater ability to withstand climate change and therefore be a good model for selection of important molecular markers.