Genômica de DNAs repetitivos em Drosophila virilis

• Ano de defesa: 2017
• Autor(a) principal: Guilherme Borges Dias
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: por
• Instituição de defesa: Universidade Federal de Minas Gerais; Brasil; ICB - INSTITUTO DE CIÊNCIAS BIOLOGICAS; Programa de Pós-Graduação em Genética; UFMG
• Palavras-chave em Português: DNAs; Genomas eucariotos; Drosophila virilis; Genômica; Mosca-das-frutas; Heterocromatina; Transposons; Sequências de Repetição em Tandem
• Link de acesso: http://hdl.handle.net/1843/56230

Repetitive DNAs represent a large fraction of eukaryote genomes. These elements are underrepresented in genomic analyses because of the computational limitations in dealing with repeats, especially with current short read sequencing technologies. Drosophila virilis is the Drosophila species with the largest genome and largest proportion of repetitive DNA among all the sequenced species of the genus. This thesis reunites efforts in characterizing repetitive DNAs of D. virilis. In the first chapter, we characterized a tandem repeat identified as the most abundant in D. virilis and discussed its origin, chromosome distribution and impact in genome evolution. We demonstrate that this repeat is a satellite DNA that emerged from internal tandem repeats from an Helitron transposon. The same phenomenon happened independently from a homologous Helitron in D. biarmipes, a phylogenetically distant species. In D. virilis, this transposon and its associated repeats are abundant in chromatin transition zones and generate piRNAs, suggesting possible chromatin modulation roles for these sequences. In the second chapter, we discuss the possible role of transposon derived repeats on genome-wide chromatin modulation. We also describe transposition models which explain the frequent tandem insertions of Helitrons, a phenomenon that has not been addressed so far. In the third and last chapter, we characterized a 172 bp tandem repeat in D. virilis. We determined that this repeat is an extremely abundant minisatellite (around 15500 copies) that is present in all species from the virilis subgroup. We also identified small RNAs derived from these repeats in embryos and gonads of D. virilis. By using long reads from third generation sequencing we produced a new genome assembly for D. virilis. This assembly proved to be a lot more contiguous than the reference genome (sequenced with the Sanger method) and recovered more complete arrays of the 172 bp tandem repeats. The results presented herein represent important additions to the characterization of repetitive DNA in the genome of D. virilis, a species traditionally used in comparative studies of the Drosophila genus.