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Sexual reproduction is an important process amongst eukaryotic organisms, with one function being to maintain genetic variation. The idea that complex eukaryotic species can persist for millions of years in the absence of sex defies fundamental evolutionary dogma, yet a group of organisms known as ancient asexuals were thought to have evolved clonally under deep evolutionary time. Prominent among these are the arbuscular mycorrhizal fungi (AMF), which are obligate plant symbionts that colonize the root cells of plants and extend their hyphae into the soil assisting the plant in acquiring key nutrients. Unlike most eukaryotes, AMF cells are multinucleate with thousands of nuclei moving through a continuous cytoplasm. Genomic analyses have identified a putative mating-type (MAT) locus within the nuclear genomes of model AMF Rhizophagus irregularis, a region that in other fungi dictates the process of sexual reproduction. Additional findings demonstrated that AMF strains carry one of two nuclear organizations. They can be either homokaryotic (AMF homokaryons), where all nuclei within the cytoplasm are virtually identical, or heterokaryotic (AMF dikaryons), where two MAT-locus variants co-exist within the cytoplasm. Despite a lack of observable traits indicative of sex, this homo/heterokaryotic dichotomy is reminiscent of the nuclear organization of sexual fungi. My research aims to build on these findings to investigate the actual role of the MAT-locus in driving AMF reproduction. To address this, I build my thesis into three main chapters. The first chapter reviews our current understanding of AMF genetics and what drives genome evolution in these organisms. The second chapter establishes a relatively easy, inexpensive, and reproducible approach to genotype known MAT variants of R. irregularis in natural and experimental conditions. The last chapter uses experimental crossings between strains to assess cytoplasmic compatibility and nuclear exchange. I demonstrate that dikaryotic spore progenies can be formed after co-culturing two distinct AMF homokaryotic strains. Further analyses of various genomic regions also reveal possible recombination in homokaryotic spore progenies from co-cultures. Overall, this research provides new experimental insights into the origin of genetic diversity in AMF. These findings open avenues to produce genetically new AMF strains in the lab using conventional crossing procedures and provide a glimpse of the mechanisms that generate AMF genetic diversity in the field.

Recombination is a genetic process of extreme importance in evolutionary biology. It creates novel haplotypes and breaks down existing ones, and can affect the levels of genetic diversity and the efficacy of selection. It also plays an important role in the evolution of sex chromosomes and the divergence process leading to speciation. Considering the particularities of the wood white (Leptidea sinapis) genome, with holocentric chromosomes, female achiasmy and a population-level cline in chromosome number, the study of its recombination landscape represents an opportunity to deepen the understanding of both this particular study system, and the underpinnings and consequences of recombination rate variation in general.  After DNA extraction and sequencing of 96 wood whites sampled across Sweden, population structure analyses were carried out together with a demographic history inference, which was used together with linkage disequilibrium information to establish the recombination rate in short intervals along the different chromosomes.  Population structure analyses showed that the sample set included 12 individuals of a cryptic species (cryptic wood white, L. juvernica) and, consistent with previous studies, a single population of L. sinapis in Sweden. Demographic inference analyses for independent scaffolds showed similar trend, with effective population size (Ne) decreasing considerably over the last 10,000 generations. The obtained recombination maps had a high resolution, and allowed for the identification of 553 putative recombination hotspots with a mean length of 3,770 bp. The genome-wide recombination rate was 9.98 cM/Mb, higher than in any vertebrate and butterfly species previously analysed, but lower than in the honey bee. A negative correlation between recombination rate and chromosome size was found, as well as a lower recombination rate on the Z chromosomes compared to the autosomes. The results are important for understanding the mechanisms underlying regional recombination rate variation in holocentric organisms and the potential for chromosome rearrangements to affect the recombination frequency, and consequently, rates and patterns of molecular evolution.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第24280号 / 医博第4896号 / 新制||医||1061(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 森田 智視, 教授 松田 道行, 教授 波多野 悦朗 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

<p> It was known, prior to this study, that there is a factor, or factors, in the centromere-proximal region of Neurospora sitophila which affect recombination near the centromere whether it is in Neurospora sitophila or transferred to Neurospora crassa. A location of this factor, or factors, was performed using tetrad and prototroph analysis. Further mapping of linkage group I of Neurospora crassa was undertaken when the Neurospora sitophila centromere-proximal region was present.</p> / Thesis / Master of Science (MSc)

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Two novel pump/probe techniques have been developed for measuring the recombination lifetime in crystalline silicon wafers. The first technique, single-beam pump/probe, uses one laser as both pump and probe. The second technique, quasi-steady state free-carrier absorption, measures lifetime under quasi-steady state conditions. These techniques are supported by a general mathematical model that predicts the experimental signal accounting for the 3D charge-carrier transport and recombination within the semiconductor. The predictions of the model are validated experimentally, and quantitative agreement is found between the model and experimental results for both techniques. The recombination lifetime measured by these techniques is verified independently using a standard pump/probe method, and the results are in agreement with this work. Single-beam pump/probe is a first-time demonstration of a technique capable of measuring lifetime in silicon using a single laser beam. It dramatically simplifies traditional pump/probe measurements by completely eliminating the second laser beam. QSS-FCA is the first quasi-steady state technique that can be calibrated in situ without the requirement of a calibrated reference wafer. The calibration constant is the free-carrier absorption cross section of silicon, which is a material constant. QSS-FCA is able to measure this cross section to a higher precision than what has been reported in the literature. Precise measurement of this constant opens up the possibility of studying more fundamental physics of silicon using QSS-FCA. / Thesis / Doctor of Philosophy (PhD)