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De La Torre A.R.,Umea University | Lin Y.-C.,Ghent University | Van De Peer Y.,Ghent University | Van De Peer Y.,University of Pretoria | And 2 more authors.
Genome Biology and Evolution | Year: 2015

The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms. © The Author(s) 2015.

Mellerowicz E.J.,Umea Plant Science Center | Gorshkova T.A.,Russian Academy of Sciences
Journal of Experimental Botany | Year: 2012

Gelatinous fibres are specialized fibres, distinguished by the presence of an inner, gelatinous cell-wall layer. In recent years, they have attracted increasing interest since their walls have a desirable chemical composition (low lignin, low pentosan, and high cellulose contents) for applications such as saccharification and biofuel production, and they have interesting mechanical properties, being capable of generating high tensional stress. However, the unique character of gelatinous layer has not yet been widely recognized. The first part of this review presents a model of gelatinous-fibre organization and stresses the unique character of the gelatinous layer as a separate type of cell-wall layer, different from either primary or secondary wall layers. The second part discusses major current models of tensional stress generation by these fibres and presents a novel unifying model based on recent advances in knowledge of gelatinous wall structure. Understanding this mechanism could potentially lead to novel biomimetic developments in material sciences. © 2011 The Author.

Fuentes S.,John Innes Center | Fuentes S.,University College London | Ljung K.,Umea Plant Science Center | Sorefan K.,John Innes Center | And 5 more authors.
Plant Cell | Year: 2012

Fruit growth and development depend on highly coordinated hormonal activities. The phytohormone gibberellin (GA) promotes growth by inducing degradation of the growth-repressing DELLA proteins; however, the extent to which DELLA proteins contribute to GA-mediated gynoecium and fruit development remains to be clarified. Here, we provide an in-depth characterization of the role of DELLA proteins in Arabidopsis thaliana fruit growth. We show that DELLA proteins are key regulators of reproductive organ size and important for ensuring optimal fertilization. We demonstrate that the seedless fruit growth (parthenocarpy) observed in della mutants can be directly attributed to the constitutive activation of GA signaling. It has been known for >75 years that another hormone, auxin, can induce formation of seedless fruits. Using mutants with complete lack of DELLA activity, we show here that auxin-induced parthenocarpy occurs entirely through GA signaling in Arabidopsis. Finally, we uncover the existence of a DELLA-independent GA response that promotes fruit growth. This response requires GIBBERELLIN-INSENSITIVE DWARF1-mediated GA perception and a functional 26S proteasome and involves the basic helix-loop-helix protein SPATULA as a key component. Taken together, our results describe additional complexities in GA signaling during fruit development, which may be particularly important to optimize the conditions for successful reproduction. © 2012 American Society of Plant Biologists. All rights reserved.

Coudert Y.,University of Cambridge | Palubicki W.,University of Cambridge | Ljung K.,Umea Plant Science Center | Novak O.,Palacky University | And 2 more authors.
eLife | Year: 2015

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot (gametophore) tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic branching pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport. © 2015 eLife Sciences Publications Ltd. All rights reserved.

De Rybel B.,Wageningen University | Adibi M.,LifeGlimmer GmbH | Adibi M.,Albert Ludwigs University of Freiburg | Adibi M.,Wageningen University | And 20 more authors.
Science | Year: 2014

Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.

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