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Begonia is one of the most diverse genera on the planet, with a species count approaching 2000 and a distribution across tropics in South America, Africa and South East Asia. The genus has occupied a vast range of niches; many highly variable growth forms can be found across the distribution, and species exhibit very diverse morphologies, even in closely related species. A recent study has revealed a putative whole genome duplication (WGD) event in the evolutionary history of Begonia, which has prompted an interest in investigating the impact gene and genome duplication has had on the diversification of Begonia. To answer questions about phenotypic and ecological diversification in Begonia, two species from South America, B. conchifolia and B. plebeja were chosen as study species based on their close phylogenetic relationship and divergent ecology and phenotype. RNA-seq data for six tissues from B. conchifolia and B. plebeja was generated using the Illumina sequencing platform, and normalised relative expression data was obtained by mapping reads to transcripts predicted from the B. conchifolia draft genome. A bioinformatics pipeline was devised to compare expression profiles across 6 different tissues between duplicated gene pairs shared between B. conchifolia and B. plebeja. Gene duplicate pairs were selected as candidates if they showed divergent expression in one species but not in another. Such duplicate pairs are suggestive of neofunctionalization in one species, providing evidence of a potential basis for phenotypic divergence and diversification between B. conchifolia and B. plebeja. Two duplicate pairs were identified as showing such divergent expression patterns as well as being functionally ecologically relevant, Chalcone Synthase and 3-Ketoacyl-CoA synthase, involved in anthocyanin biosynthesis and wax biosynthesis respectively. Investigation of expression and duplication patterns in both gene families showed the candidate gene families to be strikingly different. While 3-Ketoacyl-CoA synthase showed deeper duplications shared with outgroup taxa, Chalcone Synthase appeared to be expanded very recently, with a burst of duplications specific to the genus. 3-Ketoacyl-CoA synthase showed examples of partitioned expression by tissue for different gene family members, with at least five members of the gene family being highly expressed in one or two tissues only. Chalcone Synthase, however, showed dominance of one basal gene family member. Other Chalcone Synthase members, though expressed at lower levels, showed some evidence of reciprocal silencing in B. plebeja, though this pattern was not observed in B. conchifolia. Further investigation of the Chalcone Synthase gene family revealed lineage specific duplication in B. plebeja, and more extensive differential duplication patterns were found across other South American Begonias. Additionally, signals of positive selection were found in two branches on the Chalcone Synthase phylogeny.

Understanding the processes that have affected the diversification of herbaceous plants is fundamental to understand how flowering plants evolve, how ecosystems form and to predict the effect of climate change and geological events in plant communities. Aiming to create a strong phylogenetic framework where biogeographic and morphological hypothesis can be tested a higher level dated phylogeny of Gesneriaceae was produced. Gesneriaceae is a good study group as it has variable floral morphology, a broad distribution throughout the tropics and subtropics - represented in all non-arid tropical and subtropical hotspots of biodiversity. There are evident differences between lineages in the numbers of species, and it is comparatively well studied compared with other asterid families. In this study a consolidated taxonomic hypothesis of Gesneriaceae is suggested based on a genus level phylogeny, the ages of the main lineages of the family are presented, the effect of geological events are explored, the geographic origin of lineages are suggested and an insight into the effect of floral morphology on the evolution of the family is given. Limiting the taxonomic scope and focusing on a single family should help us better understand how flowering plants diversify.

Gene loss is the obverse of novel gene acquisition by a genome through a variety of evolutionary processes. It serves a number of functional and structural roles, compensating for the energy and material costs of gene complement expansion. A type of gene loss widespread in the lineages of plant genomes is ``fractionation" after whole genome doubling or tripling, where one of a pair or triplet of paralogous genes in parallel syntenic contexts is discarded. Based on previous mathematical work on the distribution of gap sizes caused by fractionation in synteny blocks, we studied fractionation in the evolutionary history of the allotetraploid Coffea arabica (CA) and its two diploid progenitors, C. canephora (CC) and C. eugenioides (CE), annotated genome assemblies being provided by the Arabica Coffee Genome Consortium. By taking advantage of synteny blocks produced by SynMap, we studied the fractionation process after speciation and tetraploidization events, including visualization and modelling the distribution of deletion segments, and mechanisms of deletion events. We also expanded the research to eight other plant species to verify the dominance of DNA excision over pseudigenization during the fractionation and other gene loss.

I investigated the origin of western Amazonian white-sand vegetation and the evolution of plant habitat specialization to different edaphic conditions in Neotropical lowland forests. In order to address these goals I used complementary ecological as well as molecular phylogenetic approaches. Amazonian white-sand forests harbour a flora specialized to nutrient-poor sandy soils, which is distributed as habitat-islands across the Amazon and Guiana Shield regions. This flora has been suggested to have many local and regional endemics, therefore making an important contribution to overall Neotropical plant diversity. The role of habitat specialization in the origin of this flora and its relationships with other floras within the Amazon- Guiana regions is not well understood. To shed light onto these questions, this thesis studies the floristic composition of these forests as well as molecular phylogenetic patterns of selected plant lineages containing white-sand species. The floristic study focused on the white-sand forests of the western Amazon region, which contained 1180 species of vascular plants whereas the non-white-sand Amazon and Guiana Shield dataset consisted of 26,887 vascular plant species. 77% of these species occurred outside white-sand habitats, in other habitat types of the Amazon region, while 23% were white-sand specialists. This demonstrates lower endemism in western Amazonian white-sand forests than previously estimated. 88% of the total westen Amazon white-sand specialist occur within the limits of the Guiana Shield region with the remaining 12% being endemics to the white-sand forests of the western Amazon. Within the Guiana-Shield region, Caquetá Moist Forests (56%), Guayanan Highlands (55%), and Negro-Branco Moist Forests (53%) were the biogeographic regions with the highest proportions of western Amazonian whitesand specialists. Cluster analysis of province level floristic checklists across the Amazon and Guiana regions showed that western Amazonian white-sand forests are nested within floras of the western Guiana-Shield region compared to other floras in the Amazon. Molecular phylogenetic analyses were carried out for the widespread and species-rich families Sapotaceae and Chrysobalanaceae, which display an uneven number of white-sand specialists. Sapotaceae had only three white-sand specialists but Chrysobalanaceae had a larger number of white-sand specialists (14 species). Phylogenetic analysis showed that white-sand specialist species in both studied families were scattered across the phylogenies. Both families show a marked absence of edaphic niche conservatism, suggesting that evolutionary switching amongst habitat types has been frequent. Ancestral state reconstruction of habitat specialization under a maximum likelihood approach suggests that preference for poor soils may be ancestral in these clades, especially in Chrysobalanaceae, but that the evolution of species entirely restricted to white-sand soils is in general much more recent and has multiple origins. For the white-sand flora of the western Amazon in particular, there is little evidence that it comprises ancient lineages as previously hypothesized. The historical construction of the Amazonian white sand flora is more likely to be the result of a gradual accumulation of species with different degrees of edaphic specialization, both by on-going speciation driven via habitat switching from non-white-sand specialists and via regional dispersal events after these habitats became available in regions such as the western Amazon. Edaphic transitions between different habitat types were not evolutionary constrained, which may have favoured edaphic niche evolution and the accumulation of plant species diversity in Neotropical lowland forests.

DNA content varies significantly over land plants, and is known to correlate with various aspects of plant form and function. In the present study, two measures of DNA content were examined in taxa across the land plant phylogeny: genome size (or C-value) and endopolyploidy (or endoreduplication index, EI). Additionally, the relationships between DNA content and various morphological and ecological traits were assessed. DNA content was determined for 64 liverwort species from 33 families. There was a large range in 1C-values from 0.27 to 20.46 pg, but no endopolyploidy was observed. There was no correlation between genome size and breeding system (monoecy vs. dioecy). Genome size and degree of endopolyploidy were determined for 74 moss species from 21 families. Genome sizes were constrained in this group, with 1C-values ranging from 0.25 to 1.21 pg. Endopolyploidy was high in all species except from the Sphagnaceae. Additionally, 1C-value was negatively correlated with desiccation tolerance but was not correlated with breeding system. DNA content variation was determined in 31 monilophyte (fern) species (including three horsetails) and 6 lycophyte (clubmoss) species. There was a wide range in 1C-values from 2.79 to 26.90 pg, and there was no indication of endopolyploidy in any of the species. Multivariate analyses were used to explore the relative contribution of traits and phylogenetic placement to DNA content varation in 41 angiosperm species. Six measures of DNA content (2C-value, 1Cx-value, leaf EI, stem EI, petal EI and root EI) were assessed. Phylogeny explained more of the variation observed in the six measures of DNA content than 21 ecological and morphological traits. However, many of the traits were able to explain some of the variation in DNA content, both with and without phylogeny included as a covaraite. One trait that was consistently correlated with DNA content was the association with arbuscular mycorrhizal (AM) fungi. In a controlled experiment, the EI in root cells colonized by AM fungi significantly increased compared to non-mycorrhizal plants. This thesis increases our knowledge regarding the extent and significance of variation in DNA content in land plants.

The colonization of the arid continental surface by plants was one of the milestones in Earth's history. Morphological innovations, such as the origin of complex 3D tissues, allowed the successful colonization and radiation of plants on land. The epidermis is the outermost plant tissue that constitutes the interface between the plant and the environment. Thus, the evolution of epidermal cells was crucial for the adaptation of plants on the terrestrial arid environment. I undertook a combined approach that aims to understand the evolutionary trends that drove land plant colonization and the genetic mechanisms that underlie the development of the epidermis. This approach includes: 1) analyses of plant transcription factors (TFs) families distribution and diversification, with a particular focus on the basic Helix-Loop-Helix (bHLH) TF family, and 2) functional characterization of a putatively conserved bHLH TF subfamily involved in epidermal cell development in land plants. Here, I showed that there was a stepwise increase in the number of transcription factor (TF) families and bHLH subfamilies that predated the colonization of the terrestrial surface by plants. The subsequent increase in TF number on land was through duplication within pre-existing TF families and subfamilies. Moreover, a similar trend occurred in metazoan bHLH TF, suggesting that the majority of innovation in plant and metazoan TF families occurred in the Precambrian before the Phanerozoic radiation of land plants and metazoans. Furthermore, I demonstrated that the function of IIIf bHLH TFs in controlling the development of the epidermal cell layer is conserved between liverworts and angiosperms. This suggests that IIIf bHLH TFs are ancient and conserved regulators of epidermal cell development since the early colonization of the land by plants. Moreover, these bHLH TFs were recruited during the evolution of land plants to control the development of seemingly unrelated morphological characters in specific lineages of extant land plants. The recruitment of ancient developmental regulators to control distinct and unrelated developmental processes in land plants might underlie the huge morphological and taxonomic radiation of plants on land.

京都大学 / 新制・課程博士 / 博士(生命科学) / 甲第24982号 / 生博第511号 / 新制||生||68(附属図書館) / 京都大学大学院生命科学研究科統合生命科学専攻 / (主査)教授 河内 孝之, 教授 荒木 崇, 教授 中野 雄司 / 学位規則第4条第1項該当 / Doctor of Philosophy in Life Sciences / Kyoto University / DFAM

Les Poaceae aussi appelées Graminées forment une importante famille botanique regroupant près de 12 000 espèces en plus de 700 genres dont les céréales. Cette famille présente un intérêt économique majeur car elle est importante dans la nutrition humaine et animale. De ce fait, cette famille a été très étudiée en génomique comparée depuis les années 1990 révélant une grande conservation de la structure de leur génome depuis leur divergence d’un ancêtre commun. Avec le séquençage de Brachypodium distachyon en 2009, nous avons réalisé l’analyse de son génome par l’identification de douze blocs de synténie avec les génomes séquencés du riz, du sorgho et du maïs ainsi que sept blocs de duplications partagées entre ces graminées. Ces données nous ont permis de suggérer que les cinq chromosomes modernes de Brachypodium sont issus de l’ancêtre commun des graminées constitué de douze chromosomes et ayant subi sept fusions au cours de l’évolution. Ces travaux nous ont permis de confirmer un possible génome ancêtre des graminées constitué de cinq chromosomes porteurs de près de 10 000 gènes et d’une taille minimale de près de 35Mb. Ensuite, sur la base des résultats de génomique comparée, nous nous sommes intéressés à l’évolution des différentes familles de micro-ARN (miARN). La comparaison de ces ARN non-codants réalisée pour le riz, le sorgho, le maïs et Brachypodium montre une conservation de cette famille chez les graminées avec 50% d’orthologues et 20% de paralogues. Sur la base des résultats de paléogénomique, nous avons proposé une modélisation de l’évolution des miARN qui corrobore l’hypothèse d’une origine très ancienne de ce mécanisme de « gene silencing ». Au-delà des nouvelles connaissances fondamentales générées au cours de ce travail de thèse sur l’évolution des génomes de graminées, les résultats que nous avons obtenus ont des applications potentielles dans le domaine de l’amélioration variétale, comme avec par exemple la possibilité de définir des marqueurs moléculaires de type COS (Conserved Orthologous Set). Ces marqueurs COS ont été mis en oeuvre pour l’étude de caractères agronomiques d’intérêt dans des espèces dont le génome n’est pas encore complètement séquencé comme le blé. / Poaceae also called Grasses are an important botanical family consisting in nearly 12,000 species in over 700 genres including cereals. This family is of major economic interest because it comprises cereals that are among the most important crops for human and animal nutrition. This family has been extensively studied in comparative genomics since the 1990s and showed a high degree of gene conservation among species since they diverged from a common ancestor. With the sequencing of Brachypodium distachyon in 2009, we performed an analysis of its genome by the identification of twelve synteny blocks with the sequenced genomes of rice, sorghum and maize and seven duplications blocks shared with these last grass species. These data allowed us to suggest the five chromosomes of Brachypodium are from the common ancestor composed of twelve chromosomes and having undergone seven fusions during the evolution. This work allowed us to confirm a possible grass ancestor with five chromosomes carrying almost 10,000 genes with a size of 35Mb. Then, based on these comparative genomics results, we studied more particularly the evolution of different families of microRNAs (miRNAs). The comparison of non-coding RNA from rice, sorghum, maize and Brachypodium showed conservation into this family for the grass species with 50% of orthologs and 20% of paralogs. Based on the paleogenomics results, we proposed an evolutionary scenario of miRNA genes, which supports the hypothesis of an ancient origin of this gene silencing mechanism in plants. Beyond the fundamental knowledge generated on the evolution of grass genomes during this PhD, these results have potential applications in breeding, for example with the possibility to identify COS (Conserved Orthologous Set) molecular markers. Such COS markers have been used for the study of agronomic traits in species not completely sequenced as wheat.