A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants

Post-print version of the article.

The language of children : evolution and development of secondary consciousness and language.

Proporciona una introducción sobre como los niños adquieren y utilizan el lenguaje. Hace hincapié en la explicación psicológica del desarrollo del lenguaje, pero, sin olvidar, los aspectos cognitivo, biológico y social en el desarrollo de éste, y también, considera la influencia de la escolaridad y la experiencia social.

The Kent coalfield; its evolution and development,

Mode of access: Internet.

The evolution and diversification of Dicers in plants

Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants (∼200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots. © 2006 Federation of European Biochemical Societies.

Structure and development of a Scalesia pedunculata stand in the Galapagos Islands

Stands of Scalesia pedunculata in the Galapagos Islands often develop as single-aged cohorts following episodes of mass death and regeneration. We updated earlier studies on a stand that had regenerated soon after the 1982–3 El Niño event. We quantified stem size distribution and dispersion pattern in a 0.56 ha plot near Los Gemelos on Santa Cruz Island. The plot was dominated (95% of basal area) by S. pedunculata. The stem size distribution showed the increased mean and variance for diameter (since 1987 and 1991) expected of an aging stand. Stems averaged smaller than in 1981, just before the last mass mortality episode. Large S. pedunculata stems were regularly dispersed while smaller stems were clumped and negatively associated with larger stems, implying that intraspecific competition may be important in structuring the stand. CDF Contribution Number 1008.

Starch, growth, and development in cuttings of rootstock "Paulsen 1103" from plants infested with ground pearl.

ABSTRACT The ground pearl, Eurhizococcus brasiliensis, is considered an important pest of vineyards in southern Brazil, with affected plants exhibiting leaf chlorosis, reduction in vigor, fading, and death. This study evaluated the quality of hardwood cuttings produced from plants infected (I) and not infected (NI) by ground pearl. ?Paulsen 1103? (Vitis berlandieri × Vitis rupestris) plants were grown for 29 months in brick-built raised beds either infested or not infested by ground pearl; then, 12 one-year-old branches with a maximum of 12 buds each were cut from each plant, subdivided into three portions (4 buds cutting-1), and subjected to destructive and nondestructive testing. Destructive testing comprised determining fresh and dry weight, length, internode diameters, and percentage of starch. Nondestructive testing comprised assessing the potential for bud sprouting and shoot development. Each mother plant in the I and NI beds was considered a replicate, with a total of 360 cuttings per treatment. It was observed that cuttings from infected plants had significantly lower (P<0.05) internode diameter, length, and fresh and dry weight than those of the uninfected plants. The percentage of starch content of the cuttings did not differ significantly. All cuttings showed the same percentage (100%) of bud breaking and no changes in growth and development of seedlings regardless of source. Given these results, it was concluded that vines of ?Paulsen 1103? infested with ground pearl produce smaller cuttings than those of uninfected plants but with no reduction in bud break percentage or seedling development. Key words: Margarodidae, Vitaceae, insect?plant interaction, carbohydrates. RESUMO A pérola-da-terra, Eurhizococcus brasiliensis, tem sido considerada uma importante praga dos vinhedos no sul do Brasil, sendo que as plantas atacadas manifestam clorose foliar, redução no vigor, definhamento e morte. Este trabalho teve por objetivo avaliar a qualidade de estacas lenhosas produzidas a partir do contraste de videiras infestadas (I) e não infestadas (NI) por pérola-da-terra. Após 29 meses de cultivo em canteiros de alvenaria, em presença ou ausência de pérola-da-terra, cada planta da variedade ?Paulsen 1103? (Vitis berlandieri × Vitis rupestris) foi submetida à retirada de 12 ramos de ano, com no máximo 12 gemas cada, sendo subdivididos em três porções 4 gemas estaca-1) e submetidos a avaliações destrutivas e não destrutivas. As destrutivas consistiram em determinar massas fresca e seca, comprimento, diâmetro de entrenós e percentual de amido. As avaliações não estrutivas consistiram em testar o potencial de brotação e desenvolvimento das estacas. Cada planta matriz dos canteiros I e NI foi considerada uma repetição, totalizando 360 estacas por tratamento. As estacas das plantas infestadas tiveram uma redução (P<0,05), em relação às não infestadas, em diâmetro, comprimento e massas fresca e seca. Não houve contraste significativo do percentual de amido avaliado das estacas. Quanto à brotação, destaca-se que todas as estacas apresentaram o mesmo percentual (100%), independente da origem, sem alterações no desenvolvimento e crescimento das mudas. Diante desses resultados, salienta-se que videiras ?Paulsen 1103? infestadas por pérola-da-terra produzem estacas menores, porém não há comprometimento no percentual de brotação e desenvolvimento das mudas, quando comparadas com plantas não infestadas. Palavras-chave: Margarodidae, Vitaceae, interação inseto-planta, carboidrato

Regulation of woody plant development by auxin and polar auxin transport

Auxin is a key regulator in plant growth and development. This dissertation examines the role of auxin and polar auxin transport in woody growth and development. Strategies of promoter reporter system, microarray expression analysis, transgenic modification, physiological assays, anatomical analysis, and histochemical/biochemical assays were employed to improve our understanding of auxin study in Populus. The results demonstrate various aspects of auxin regulation on shoot growth, root development, wood formation, and gravitropism in woody tissues. We describe the behavior of the DR5 reporter system for measuring auxin concentrations and response in stably transformed Populus trees. Our study shows that DR5 reporter system can be efficiently used in Populus to study auxin biology at a cellular resolution. We investigated the global gene expression in responding to auxin in Populus root. The results revealed groups of IBA up- and down- regulated genes involved in various biological processes including cell wall modification, root growth and lateral root formation, transporter activity and hormone crosstalk. We also verify two of the identified genes' function by transgenic modification in Populus, which encode auxin efflux carrier PtPIN9 and transcription factor PtERF72. We investigated the role of PtPIN9 in woody growth and development, especially in wood formation and gravitropic response in woody stem. We found that overexpressing PtPIN9 enhanced several growth parameters while suppression of PtPIN9 has inhibited tension wood formation. Our results show that PIN9 and other members from PIN family could be possible useful tools for increasing biomass productivity, wood quality, or in modifying plant form.

Sea Urchin Body Plan Development and Evolution: An Integrative Transcriptomic Approach

My dissertation work integrates comparative transcriptomics and functional analyses to investigate gene expression changes underlying two significant aspects of sea urchin evolution and development: the dramatic developmental changes associated with an ecologically significant shift in life history strategy and the development of the unusual radial body plan of adult sea urchins.

In Chapter 2, I investigate evolutionary changes in gene expression underlying the switch from feeding (planktotrophic) to nonfeeding (lecithotrophic) development in sea urchins. In order to identify these changes, I used Illumina RNA-seq to measure expression dynamics across 7 developmental stages in three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph Heliocidaris tuberculata, and an outgroup planktotroph Lytechinus variegatus. My analyses draw on a well-characterized developmental gene regulatory network (GRN) in sea urchins to understand how the ancestral planktotrophic developmental program was altered during the evolution of lecithotrophic development. My results suggest that changes in gene expression profiles occurred more frequently across the transcriptome during the evolution of lecithotrophy than during the persistence of planktotrophy. These changes were even more pronounced within the GRN than across the transcriptome as a whole, and occurred in each network territory (skeletogenic, endomesoderm and ectoderm). I found evidence for both conservation and divergence of regulatory interactions in the network, as well as significant changes in the expression of genes with known roles in larval skeletogenesis, which is dramatically altered in lecithotrophs. I further explored network dynamics between species using coexpression analyses, which allowed me to identify novel players likely involved in sea urchin neurogenesis and endoderm patterning.

In Chapter 3, I investigate developmental changes in gene expression underlying radial body plan development and metamorphosis in H. erythrogramma. Using Illumina RNA-seq, I measured gene expression profiles across larval, metamorphic, and post-metamorphic life cycle phases. My results present a high-resolution view of gene expression dynamics during the complex transition from pre- to post-metamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases.

Collectively, my investigations provide an important foundation for future, empirical studies to investigate the functional role of gene expression change in the evolution of developmental differences between species and also for the generation of the unusual radial body plan of sea urchins.

Evolution of the rbcS gene family in Solanaceae: concerted evolution and gain and loss of introns, with a description of new statistical guidelines for determining the number of unique gene copies.

Thesis (Ph.D.)--University of Washington, 2014

A phylogenomics approach to resolving fungal evolution, and phylogenetic method development

Bien que les champignons soient régulièrement utilisés comme modèle d'étude des systèmes eucaryotes, leurs relations phylogénétiques soulèvent encore des questions controversées. Parmi celles-ci, la classification des zygomycètes reste inconsistante. Ils sont potentiellement paraphylétiques, i.e. regroupent de lignées fongiques non directement affiliées. La position phylogénétique du genre Schizosaccharomyces est aussi controversée: appartient-il aux Taphrinomycotina (précédemment connus comme archiascomycetes) comme prédit par l'analyse de gènes nucléaires, ou est-il plutôt relié aux Saccharomycotina (levures bourgeonnantes) tel que le suggère la phylogénie mitochondriale? Une autre question concerne la position phylogénétique des nucléariides, un groupe d'eucaryotes amiboïdes que l'on suppose étroitement relié aux champignons. Des analyses multi-gènes réalisées antérieurement n'ont pu conclure, étant donné le choix d'un nombre réduit de taxons et l'utilisation de six gènes nucléaires seulement. Nous avons abordé ces questions par le biais d'inférences phylogénétiques et tests statistiques appliqués à des assemblages de données phylogénomiques nucléaires et mitochondriales. D'après nos résultats, les zygomycètes sont paraphylétiques (Chapitre 2) bien que le signal phylogénétique issu du jeu de données mitochondriales disponibles est insuffisant pour résoudre l'ordre de cet embranchement avec une confiance statistique significative. Dans le Chapitre 3, nous montrons à l'aide d'un jeu de données nucléaires important (plus de cent protéines) et avec supports statistiques concluants, que le genre Schizosaccharomyces appartient aux Taphrinomycotina. De plus, nous démontrons que le regroupement conflictuel des Schizosaccharomyces avec les Saccharomycotina, venant des données mitochondriales, est le résultat d'un type d'erreur phylogénétique connu: l'attraction des longues branches (ALB), un artéfact menant au regroupement d'espèces dont le taux d'évolution rapide n'est pas représentatif de leur véritable position dans l'arbre phylogénétique. Dans le Chapitre 4, en utilisant encore un important jeu de données nucléaires, nous démontrons avec support statistique significatif que les nucleariides constituent le groupe lié de plus près aux champignons. Nous confirmons aussi la paraphylie des zygomycètes traditionnels tel que suggéré précédemment, avec support statistique significatif, bien que ne pouvant placer tous les membres du groupe avec confiance. Nos résultats remettent en cause des aspects d'une récente reclassification taxonomique des zygomycètes et de leurs voisins, les chytridiomycètes. Contrer ou minimiser les artéfacts phylogénétiques telle l'attraction des longues branches (ALB) constitue une question récurrente majeure. Dans ce sens, nous avons développé une nouvelle méthode (Chapitre 5) qui identifie et élimine dans une séquence les sites présentant une grande variation du taux d'évolution (sites fortement hétérotaches - sites HH); ces sites sont connus comme contribuant significativement au phénomène d'ALB. Notre méthode est basée sur un test de rapport de vraisemblance (likelihood ratio test, LRT). Deux jeux de données publiés précédemment sont utilisés pour démontrer que le retrait graduel des sites HH chez les espèces à évolution accélérée (sensibles à l'ALB) augmente significativement le support pour la topologie « vraie » attendue, et ce, de façon plus efficace comparée à d'autres méthodes publiées de retrait de sites de séquences. Néanmoins, et de façon générale, la manipulation de données préalable à l'analyse est loin d’être idéale. Les développements futurs devront viser l'intégration de l'identification et la pondération des sites HH au processus d'inférence phylogénétique lui-même.

Amphioxus molecular biology: insights into vertebrate evolution and developmental mechanisms

The cephalochordate amphioxus is the best available proxy for the last common invertebrate ancestor of the vertebrates. During the last decade, the developmental genetics of amphioxus have been extensively examined for insights into the evolutionary origin and early evolution of the vertebrates. Comparisons between expression domains of homologous genes in amphioxus and vertebrates have strengthened proposed homologies between specific body parts. Molecular genetic studies have also highlighted parallels in the developmental mechanisms of amphioxus and vertebrates. In both groups, a similar nested pattern of Hox gene expression is involved in rostrocaudal patterning of the neural tube, and homologous genes also appear to be involved in dorsoventral neural patterning. Studies of amphioxus molecular biology have also hinted that the protochordate ancestor of the vertebrates included cell populations that modified their developmental genetic pathways during early vertebrate evolution to yield definitive neural crest and neurogenic placodes. We also discuss how the application of expressed sequence tag and gene-mapping approaches to amphioxus have combined with developmental studies to advance our understanding of chordate genome evolution. We conclude by considering the potential offered by the sequencing of the amphioxus genome, which was completed in late 2004.

Independent fusions and recent origins of sex chromosomes in the evolution and diversification of glass knife fishes (Eigenmannia)

The genus Eigenmannia comprises several species groups that display a surprising variety of diploid chromosome numbers and sex-determining systems. In this study, hypotheses regarding phylogenetic relationships and karyotype evolution were investigated using a combination of molecular and cytogenetic methods. Phylogenetic relationships were analyzed for 11 cytotypes based on sequences from five mitochondrial DNA regions. Parsimony-based character mapping of sex chromosomes confirms previous suggestions of multiple origins of sex chromosomes. Molecular cytogenetic analyses involved chromosome painting using probes derived from whole sex chromosomes from two taxa that were hybridized to metaphases of their respective sister cytotypes. These analyses showed that a multiple XY system evolved recently (<7 mya) by fusion. Furthermore, one of the chromosomes that fused to form the neo-Y chromosome is fused independently to another chromosome in the sister cytotype. This may constitute an efficient post-mating barrier and might imply a direct function of sex chromosomes in the speciation processes in Eigenmannia. The other chromosomal sex-determination system investigated is shown to have differentiated by an accumulation of heterochromatin on the X chromosome. This has occurred in the past 0.6 my, and is the most recent chromosomal sex-determining system described to date. These results show that the evolution of sex-determining systems can proceed very rapidly. Heredity (2011) 106, 391-400; doi:10.1038/hdy.2010.82; published online 23 June 2010