Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (rho), sigma (sigma), and tau (tau), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23047号 / 理博第4724号 / 新制||理||1677(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 田村 実, 教授 鹿内 利治, 教授 工藤 洋 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

<p>This thesis concerns different aspects of dating divergence times in phylogenetic trees, using molecular data and multiple fossil age constraints.</p><p>Datings of phylogenetically basal eudicots, monocots and modern birds (Neoaves) are presented. Large phylograms and multiple fossil constraints were used in all these studies. Eudicots and monocots are suggested to be part of a rapid divergence of angiosperms in the Early Cretaceous, with most families present at the Cretaceous/Tertiary boundary. Stem lineages of Neoaves were present in the Late Cretaceous, but the main divergence of extant families took place around the Cre-taceous/Tertiary boundary.</p><p>A novel method and computer software for dating large phylogenetic trees, PATHd8, is presented. PATHd8 is a nonparametric smoothing method that smoothes one pair of sister groups at a time, by taking the mean of the added branch lengths from a terminal taxon to a node. Because of the local smoothing, the algorithm is simple, hence providing stable and very fast analyses, allowing for thousands of taxa and an arbitrary number of age constraints.</p><p>The importance of fossil constraints and their placement are discussed, and concluded to be the most important factor for obtaining reasonable age estimates.</p><p>Different dating methods are compared, and it is concluded that differences in age estimates are obtained from penalized likelihood, PATHd8, and the Bayesian autocorrelation method implemented in the multidivtime program. In the Bayesian method, prior assumptions about evolutionary rate at the root, rate variance and the level of rate smoothing between internal edges, are suggested to influence the results.</p>

This thesis concerns different aspects of dating divergence times in phylogenetic trees, using molecular data and multiple fossil age constraints. Datings of phylogenetically basal eudicots, monocots and modern birds (Neoaves) are presented. Large phylograms and multiple fossil constraints were used in all these studies. Eudicots and monocots are suggested to be part of a rapid divergence of angiosperms in the Early Cretaceous, with most families present at the Cretaceous/Tertiary boundary. Stem lineages of Neoaves were present in the Late Cretaceous, but the main divergence of extant families took place around the Cre-taceous/Tertiary boundary. A novel method and computer software for dating large phylogenetic trees, PATHd8, is presented. PATHd8 is a nonparametric smoothing method that smoothes one pair of sister groups at a time, by taking the mean of the added branch lengths from a terminal taxon to a node. Because of the local smoothing, the algorithm is simple, hence providing stable and very fast analyses, allowing for thousands of taxa and an arbitrary number of age constraints. The importance of fossil constraints and their placement are discussed, and concluded to be the most important factor for obtaining reasonable age estimates. Different dating methods are compared, and it is concluded that differences in age estimates are obtained from penalized likelihood, PATHd8, and the Bayesian autocorrelation method implemented in the multidivtime program. In the Bayesian method, prior assumptions about evolutionary rate at the root, rate variance and the level of rate smoothing between internal edges, are suggested to influence the results.

Les angiospermes (ou plantes à fleurs) regroupent environ 350 000 espèces ayant divergé il y a 150 à 200 millions d’années en deux familles botaniques principales, les monocotylédones (les orchidées, les palmiers, les bananiers, les joncs, les graminées...) et les eudicotylédones (les Brassicaceae, les Rosaceae, les légumineuses...) représentant respectivement 20% et 75% des plantes à fleurs. Les angiospermes font l’objet de nombreux travaux de recherche, en particulier en génomique depuis 2000 avec le séquençage du premier génome de plantes (Arabidopsis thaliana) qui a précédé le décryptage des génomes d’un nombre important d’autres espèces modèles et/ou d’intérêt agronomique (environ 100 aujourd’hui). L’accès croissant à la séquence des génomes de plantes a permis de mettre à jour une importante diversité structurale de leur génome, en termes de taille physique, de nombre de chromosomes, de nombre de gènes et de richesse en éléments transposables. Les forces évolutives ayant permis une telle diversité structurale des génomes au cours de l’évolution sont au cœur des travaux de cette thèse. La paléogénomique se propose d’étudier à travers la reconstruction de génomes ancestraux, comment ces espèces ont divergé à partir d’ancêtres communs et quels mécanismes ont contribué à une telle plasticité de structure génomique. Dans cet objectif, les travaux de cette thèse ont mis en œuvre des méthodes basées sur la génomique comparée permettant l’étude de l’évolution structurale des génomes via la reconstruction des génomes ancestraux fondateurs des espèces modernes. Ainsi, un génome ancestral des angiospermes a été reconstruit constitué de 5 chromosomes et porteur de 6707 gènes ordonnés sur ceux-ci, permettant d’intégrer dans un même modèle les monocotylédones et les eudicotylédones et élucider leur histoire évolutive, notamment pour les espèces d’intérêt agronomique majeur telles que les céréales, les rosids et les Brassicaceae. L’inférence de ces génomes ancestraux des plantes modernes a permis l’identification et l’étude de l’impact des évènements de polyploïdie (doublement génomique), ubiquitaires chez les plantes. Nous avons montré que les génomes tendent à revenir à une structure diploïde suite à un évènement de polyploïdie. Cette diploïdisation structurale se fait au niveau caryotypique (par le biais de réarrangements chromosomiques impliquant la perte des centromères et télomères ancestraux) mais aussi géniques (par le biais de pertes de gènes ancestraux en double copies). Il a été montré que cette perte se faisait préférentiellement sur un des sous-génomes post-polyploïdie, menant au phénomène de « dominance des sous-génomes ». Ces biais de plasticité structurale (on parle de compartimentation de la plasticité) se font différentiellement entre les espèces, les chromosomes, les compartiments chromosomiques mais aussi les types de gènes, aboutissant à la diversité structurale observée entre les génomes modernes de plantes. Ces travaux qui rentrent dans le cadre de la recherche fondamentale ont également un fort aspect appliqué à travers la recherche translationnelle en ayant permis de créer des passerelles entre les différentes espèces travaillées en agriculture. Le passage d’une espèce à une autre via les génomes ancestraux fondateurs reconstruits permet notamment le transfert de connaissances des gènes ou de régions d’intérêt des espèces modèles aux espèces cultivées. Les travaux de thèse, par la reconstruction d’ancêtres, permettent une comparaison de haute-résolution des génomes de plantes et in fine l’étude de leur plasticité acquise au cours de l’évolution, et revêtent donc à la fois un aspect fondamental (pour comprendre l’évolution des espèces) mais aussi appliqué (pour l’amélioration des espèces d’intérêt agronomique à partir des modèles). / Angiosperms (or flowering plants) consist in approximatively 350 000 species that have diverged 150 to 200 million years ago in two main families, monocots (orchids, palm trees, banana, bulrushes, grasses...) and dicots (Brassicaceae, Rosaceae, legumes...) representing respectively 20% and 75% of flowering plants. Angiosperms are the subject of intense researches, in particular in genomics since 2000 with the sequence release of the first plant genome (Arabidopsis thaliana) preceding a large number of genomes of plant models and/or species of agronomical interest (around 100 today). Increasing access to plant genome sequences has allowed the identification of their structural diversity, in terms of genome size, number of chromosomes and genes as well as transposable element content. The evolutionary forces that have shaped such structural genomic divergence are at the center of this thesis. Our paleogenomics approach will investigate, through ancestral genome reconstructions, how modern species have diverged from common ancestors and which mechanisms have contributed to such present-day genome plasticity. In this thesis, we have developed methods based on comparative genomics to study plant genome evolution and reconstruct ancestral genomes, extinct progenitors of the modern angiosperm species. An ancestral angiosperm genome has been reconstructed made of 5 chromosomes and 6707 ordered genes allowing the integration in the same model of monocots and eudicots and finally elucidating evolutionary trajectories for species of major agricultural interest such as cereals, rosids and Brassicaceae. The reconstructed paleohistory of modern flowering plants enabled the identification as well as the investigation of the impact of polyploidy events (WGD, whole genome duplications), ubiquitous in plants, as a major driver of the observed structural plasticity of angiosperms. We established that genomes tend to return to a diploid status following a polyploidy event. This structural diploidization is performed at the karyotypic level through chromosomal rearrangements (involving ancestral centromeres and telomeres losses) as well as the gene level (through ancestral duplicates loss). It has been shown that this diploidization is preferentially done on one of the post-polyploidy subgenome, leading to the "sub-genome dominance" phenomenon. This structural plasticity bias (also referenced as plasticity partitioning) is acting differentially between species, chromosomes, chromosomal compartments, gene types, resulting in the structural diversity observed between the present-day plant genomes. This thesis is clearly within the scope of fundamental researches but also has a strong applied objective through translational research in creating bridges between species of major relevance for agriculture. The comparison of one species to another through the reconstructed ancestral genomes allows transferring knowledge gained on genes or any region of interest from model species to crops. Paleogenomics, in reconstructing ancestral genome and unveiling the forces driving modern plant genome plasticity, is therefore of fundamental (toward understanding species evolution) but also applied (toward improving orphan species from knowledge gained in models) objectives.

No description available.

Данная работа содержит 52 страницы машинописного текста, включая 19 рисунков, 1 таблицу и 106 литературных источников. Работа посвящена изучению разнообразия совокупности признаков корней четырех семейств однодольных растений – Orchidaceae Juss., Iridaceae L., Poaceae Barnhart и Cyperaceae Juss., в условиях бореальной климатической зоны. В анализ вошли материалы, предоставленные научным руководителем (данные по строению корней представителей семейств Orchidaceae, Poaceae, Cyperaceae) и оригинальные сборы. Цель – выявить разнообразие синдромов корневых признаков у четырех семейств однодольных растений бореальной зоны. Для достижения цели были поставлены следующие задачи: изучить строение поглощающих корней представителей семейств Orchidaceae, Iridaceae, Poaceae, Cyperaceae; изучить внешние признаки корневых систем представителей семейств Orchidaceae, Iridaceae, Poaceae, Cyperaceae; сравнить комплекс количественных и качественных признаков в масштабе всей корневой системы у таксонов с разными типами микориз, а также с преобладанием немикоризных видов. С помощью классических методов структурной ботаники были изучены внешние признаки корневых систем и строение поглощающих корней. Получали микротомные срезы поглощающих корней, которые анализировали под микроскопом Leica DM 5000 в светлом поле и в синих лучах длиной волны 365 нм (флуоресцентная микроскопия). С помощью окулярмикрометра измеряли диаметр корня и стелы, толщину коры, длину корневых волосков, подсчитывали число сосудов ксилемы. На продольных препаратах определяли встречаемость корневых волосков. Число порядков ветвления корневой системы фиксировали по функциональной классификации [McCormack et al., 2015]. Установление микоризации выполняли методом световой микроскопии (Leica DM 5000; ×100) после предварительной мацерации корней в КОН и окрашивания анилиновым синим [Селиванов, 1981]. Обработка данных производилась в программе EXCEL, а с помощью программы STATISTICA был проведен однофакторный дисперсионный анализ ANOVA. Результаты исследований показали, что корни разных таксонов однодольных сильно различаются по внешнему и внутреннему строению. Были выявлены синдромы корневых признаков: Orchidaceae – толстые не ветвящиеся корни с сильно развитой специализированной микоризой, с относительно толстой корой и стелой, длинными корневыми волосками и без выраженной экзодермы; Iridaceae – толстые сильно разветвленные корни с мощной экзодермой, короткими редко встречающимися корневыми волосками и интенсивной АМ; Poaceae – тонкие разветвленные корни с невыраженной экзодермой, с короткими, часто встречающимися корневыми волосками и интенсивной АМ; Cyperaceae – тонкие, сильно разветвленные корни с хорошо развитыми корневыми волосками и другими приспособлениями к автономному почвенному питанию, АМ встречается редко. / This work contains 52 pages of typewritten text, including 19 figures, 1 table and 106 literature sources. The work is devoted to the study of the diversity of the totality of the traits of the roots of four families of monocotyledonous plants – Orchidaceae Juss., Iridaceae L., Poaceae Barnhart and Cyperaceae Juss., in the conditions of the boreal climatic zone. The analysis included materials provided by the scientific advisor (data on the structure of roots of representatives of the families Orchidaceae, Poaceae, Cyperaceae) and original collections. The goal is to identify the diversity of root trait syndromes in four families of monocotyledonous plants in the boreal zone. To achieve the goal, the following tasks were set: to study the structure of absorbing roots of representatives of the families Orchidaceae, Iridaceae, Poaceae, Cyperaceae; to study the external signs of root systems of representatives of the families Orchidaceae, Iridaceae, Poaceae, Cyperaceae; to compare the complex of quantitative and qualitative characters on the scale of the entire root system in taxa with different types of mycorrhizal, as well as with a predominance of nonmycorrhizal species. Using classical methods of structural botany, the external signs of root systems and the structure of absorbing roots were studied. Received microtome sections of absorbing roots, which were analyzed under a Leica DM 5000 microscope in a bright field and in blue beams with a wavelength of 365 nm (fluorescence microscopy). Using an eyepiece micrometer, the following was measured: the diameter of the root and stele, the thickness of the cortex, the length of root hairs, and the number of xylem vessels was counted. On longitudinal preparations, the occurrence of root hairs was determined. The number of orders of branching of the root system was fixed according to the functional classification [McCormack et al., 2015]. Mycorrhiza was determined by light microscopy (Leica DM 5000; × 100) after preliminary maceration of the roots in KOH and staining with aniline blue [Selivanov, 1981]. The data were processed using the EXCEL program, and the one-way ANOVA was carried out using the STATISTICA program. The research results showed that the roots of different monocotyledonous taxa differ greatly in their external and internal structure. Syndromes of root signs were identified: Orchidaceae – thick non-branching roots of with highly developed specialized mycorrhiza, with relatively thick bark and stele, long root hairs and without pronounced exoderm; Iridaceae – thick, highly branched roots of with powerful exoderm, short rare root hairs and intense AM; Poaceae – thin branched roots of with an indistinct exoderm, with short, frequently occurring root hairs and intense AM; Cyperaceae – thin, highly branched roots of with well-developed root hairs and other adaptations to autonomous soil nutrition, AM is rare.