A framework for orthology assignment from gene rearrangement data

Abstract. Gene rearrangements have successfully been used in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive when comparing nuclear genomes. The main challenge is how to deal with gene families, specifically, how to identify orthologs. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. We approach that problem using gene rearrangement data, provide an optimization framework in which to phrase the problem, and present some preliminary theoretical results.

A scenario of mitochondrial genome evolution in maize based on rearrangement events

Background: Despite their monophyletic origin, animal and plant mitochondrial genomes have been described as exhibiting different modes of evolution. Indeed, plant mitochondrial genomes feature a larger size, a lower mutation rate and more rearrangements than their animal counterparts. Gene order variation in animal mitochondrial genomes is often described as being due to translocation and inversion events, but tandem duplication followed by loss has also been proposed as an alternative process. In plant mitochondrial genomes, at the species level, gene shuffling and duplicate occurrence are such that no clear phylogeny has ever been identified, when considering genome structure variation. Results: In this study we analyzed the whole sequences of eight mitochondrial genomes from maize and teosintes in order to comprehend the events that led to their structural features, i.e. the order of genes, tRNAs, rRNAs, ORFs, pseudogenes and non-coding sequences shared by all mitogenomes and duplicate occurrences. We suggest a tandem duplication model similar to the one described in animals, except that some duplicates can remain. Thi

Filogeografia comparada na floresta atlântica usando sequenciamento de nova geração

Orientador : Prof. Dr. Mario R. PieTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Biológicas, Programa de Pós-Graduação em Ciências Biológicas (Entomologia). Defesa: Curitiba, 24/02/2017Inclui referênciasÁrea de concentração : EntomologiaResumo: Esta tese usa a filogeografia comparada como ferramenta para o melhor entendimento do passado evolutivo da Floresta Atlântica, um ambiente de rica biodiversidade e reconhecido mundialmente pelos seus altos índices de endemismo. Para cumprir tal tarefa foi realizado um estudo mirmecológico com várias espécies cujas a distribuições geográficas contemplam quase a totalidade da distribuição Norte/Sul do bioma. Além de ser um estudo pioneiro com filogeografia comparada em invertebrados neste ambiente, destaca-se o uso do sequenciamento de nova geração para a obtenção de centenas de loci para cada indivíduo em busca de uma visão mais ampla de suas informações genéticas. Devido a estas características o primeiro capítulo desta tese apresenta uma revisão em sequenciamento de DNA e suas aplicações em entomologia a fim de familiarizar o leitor aos métodos utilizados no estudo. Com esta mesma finalidade o segundo capítulo é dedicado ao maior entendimento dos marcadores utilizados nas análises moleculares, os Elementos Ultraconservados. O terceiro capítulo é a primeira descrição de um genoma mitocondrial para o gênero Octostruma, resultado que só foi possível graças ao método de sequenciamento utilizado e que exemplifica o poder das novas tecnologias mesmo em organismos não-modelo. Finalmente, o quarto capítulo agrega aos resultados filogeográficos dados de modelagem de nicho para revelar como diferentes espécies responderam às mudanças climáticas durante o Quaternário. Em particular, mostramos que o padrão de distribuição da variabilidade genética na Floresta Atlântica é o produto complexo de fatores históricos (ex. mudanças na extensão das florestas úmidas, disponibilidade de refúgios) e as características biológicas de cada espécie (ex. hábito, capacidade de dispersão, nicho climático ancestral). Palavras-chave: Filogeografia, Elementos Ultraconservados, Floresta Atlântica.Abstract: This dissertation uses comparative phylogeography as a tool to better understand the Brazilian Atlantic Rainforest evolutionary past, a place of enormous biodiversity and well known for its high endemism level. To perform this task a myrmecological study was carried out with several species whose geographical distributions span the North/South forest range. It is a pioneering study in this biome using invertebrate's comparative phylogeography and is also novel in the use of new sequencing technologies to obtain hundreds of loci for each individual to provide a broad view of its genetics. Because such singularity the first chapter introduces and reviews the history of DNA sequencing and its applications to entomology, the goal here is to provide to the reader a background about this dissertation's methods. With the same aim, the second chapter is dedicated to present the Ultraconserved Elements, that were used in the molecular analyses. Third chapter is the first description for the mitochondrial genome in the Octostruma genus, a result that was only possible because of the sequencing method applied to the study and exemplifies the power of new technologies even to non-model organisms. Finally, the fourth chapter integrates phylogeographical results with environmental niche modeling to reveal how different species responded to the climatic changes during the Quaternary. In particular, we show that the pattern of distribution of genetic variability in the Atlantic Forest is the complex outcome of historical factors (e.g. changes in the extent of humid forests, availability of refugia) and biological characteristics of each species (e.g. habit, dispersal capacity, ancestral climatic niche). Key words: Phylogeography, Ultraconservative Elements, Atlantic Rainfores

Early eukaryote evolution based on mitochondrial gene order breakpoints

We present a general heuristic for the median problem for induced breakpoints on genomes with unequal gene con-tent and incorporate this into a routine for estimating op-timal gene orders for the ancestral genomes in a fixed phy-logeny. The routine is applied to a phylogenetic study of an up-to-date set of completely sequenced protist mitochon-drial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, con-firming the usefulness of the breakpoint method as a phylo-genetic tool even for small genomes. 1 Introduction. The origin and early diversification of the eukaryotes is one of the fundamental problems of evolutionary theory. The widely accepted endosymbiotic origin of the mitochondrio

Mathematical models for evolution of genome structure

The structure of a genome can be characterized by its gene content. Evolution of genome structure in closely related species can be studied by examining their synteny or conserved gene order and content. A variety of evolutionary rearrangements like polyploidy, inversions, transpositions, translocations, gene duplication and gene loss degrade synteny over time. In this dissertation, I approach the problem of understanding synteny in genomes and how far back its evolutionary history can be traced in multiple ways. First, I present a probabilistic model of the rearrangements gene loss and transposition (gain) and apply it to the problem of estimating the relative contribution of these rearrangements within a set of syntenic genome segments. This model can be used to predict gene content in syntenic regions of unsequenced genomes. Next, I use optimization methods to recover syntenic segments between genomes based on reconstructions of their parent ancestry. I examine how these reconstructions can be used as input to programs that identify syntenic regions in genomes to reveal more synteny than was previously detected. I use simulations that incorporate each of the evolutionary rearrangements described above to evaluate the models presented in this dissertation. Finally, I apply these models to genomic data from yeast and flowering plants, two eukaryotic systems that are known to have experienced polyploidy. This application is of particular relevance in flowering plants, in which a lot of economically and scientifically important polyploid species have incompletely sequenced genomes

Species of Phytophthora associated with a native ecosystem in Gauteng

Access to this dissertation is restricted until 2015-04-12Dissertation (MSc)--University of Pretoria, 2012.GeneticsMScUnrestricte