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Toxic algae species is full of freeloading cheaters... and why that makes them even deadlier

Toxic algae species is full of freeloading cheaters... and why that makes them even deadlier | Plant Gene Seeker -PGS | Scoop.it
Prymnesium parvum is a single-celled, toxic algae species that wreaks havoc throughout U.S. waters. The toxin is designed to wipe out their competition for sunlight and nutrients...

 

Nice story, here's the article: http://onlinelibrary.wiley.com/doi/10.1111/evo.12030/abstract


Via Mary Williams
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Mary Williams's curator insight, February 1, 2013 12:22 PM

I love this video "Golden algae attacking" - Prymnesium parvum algae ganging up on a marine green alga... http://www.eurekalert.org/pub_releases/2013-01/uoa-tht011813.php. Show your students, they'll love it and want to learn more!

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The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Andres Zurita's insight:

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

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CONSTANS-LIKE 7 (COL7) Is Involved in Phytochrome B (phyB)-Mediated Light-Quality Regulation of Auxin Homeostasis

CONSTANS-LIKE 7 (COL7) Is Involved in Phytochrome B (phyB)-Mediated Light-Quality Regulation of Auxin Homeostasis | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Arabidopsis phytochrome B (phyB) is the major photoreceptor that senses the ratio of red to far-red light (R:FR) to regulate the shade-avoidance response (SAR). It has been hypothesized that altered homeostasis of phytohormones such as auxin and strigolactone is at least partially responsible for SAR, but the mechanism underlying phyB regulation of the hormonal change is not fully understood. Previously we reported thatCONSTANS-LIKE 7 (COL7) enhances branching number under high R:FR but not under low R:FR, implying that COL7 may be involved in the phyB-mediated SAR. In this study, we provide evidence that COL7 reduces auxin levels in a high R:FR-dependent manner. We found that the phyB mutation suppresses the COL7-induced branching proliferation. Moreover, COL7 promotes mRNA expression of SUPERROOT 2 (SUR2), which encodes a suppressor of auxin biosynthesis, in high R:FR but not in low R:FR. Consistently with these results, deficiency of phyB suppresses the elevated transcription of SUR2 in COL7 overexpression plants grown in high R:FR.

Taking these results together with data suggesting that photo-excited phyB is required for stabilization of the COL7 protein, we argue that COL7 is a critical factor linking light perception to changes in auxin level in Arabidopsis.

 
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OSCA1 mediates osmotic-stress-evoked Ca2+ increases vital for osmosensing in Arabidopsis

OSCA1 mediates osmotic-stress-evoked Ca2+ increases vital for osmosensing in Arabidopsis | Plant Gene Seeker -PGS | Scoop.it

Water is crucial to plant growth and development. Environmental water deficiency triggers an osmotic stress signalling cascade, which induces short-term cellular responses to reduce water loss and long-term responses to remodel the transcriptional network and physiological and developmental processes1, 2, 3, 4. Several signalling components that have been identified by extensive genetic screens for altered sensitivities to osmotic stress seem to function downstream of the perception of osmotic stress. It is known that hyperosmolality and various other stimuli trigger increases in cytosolic free calcium concentration ([Ca2+]i)5, 6. Considering that in bacteria and animals osmosensing Ca2+ channels serve as osmosensors7, 8, hyperosmolality-induced [Ca2+]i increases have been widely speculated to be involved in osmosensing in plants1, 9. However, the molecular nature of corresponding Ca2+ channels remain unclear6, 10, 11. Here we describe a hyperosmolality-gated calcium-permeable channel and its function in osmosensing in plants. Using calcium-imaging-based unbiased forward genetic screens we isolated Arabidopsis mutants that exhibit low hyperosmolality-induced [Ca2+]i increases. These mutants were rescreened for their cellular, physiological and developmental responses to osmotic stress, and those with clear combined phenotypes were selected for further physical mapping. One of the mutants, reduced hyperosmolality-induced [Ca2+]i increase 1 (osca1), displays impaired osmotic Ca2+ signalling in guard cells and root cells, and attenuated water transpiration regulation and root growth in response to osmotic stress. OSCA1 is identified as a previously unknown plasma membrane protein and forms hyperosmolality-gated calcium-permeable channels, revealing that OSCA1 may be an osmosensor. OSCA1 represents a channel responsible for [Ca2+]i increases induced by a stimulus in plants, opening up new avenues for studying Ca2+ machineries for other stimuli and providing potential molecular genetic targets for engineering drought-resistant crops.


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Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.)

Construction and validation of a gene co-expression network in grapevine (Vitis vinifera. L.) | Plant Gene Seeker -PGS | Scoop.it
Horticulture Research, Published online: 13 August 2014; | doi:10.1038/hortres.2014.40
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Gene co-expression analysis has been widely used for predicting gene functions because genes within modules of a co-expression network may be involved in similar biological processes and exhibit similar biological functions. To detect gene relationships in the grapevine genome, we constructed a grapevine gene co-expression network (GGCN) by compiling a total of 374 publically available grapevine microarray datasets. The GGCN consisted of 557 modules containing a total of 3834 nodes with 13 479 edges. The functions of the subnetwork modules were inferred by Gene ontology (GO) enrichment analysis. In 127 of the 557 modules containing two or more GO terms, 38 modules exhibited the most significantly enriched GO terms, including ‘protein catabolism process’, ‘photosynthesis’, ‘cell biosynthesis process’, ‘biosynthesis of plant cell wall’, ‘stress response’ and other important biological processes. The ‘response to heat’ GO term was highly represented in module 17, which is composed of many heat shock proteins. To further determine the potential functions of genes in module 17, we performed a Pearson correlation coefficient test, analyzed orthologous relationships with Arabidopsis genes and established gene expression correlations with real-time quantitative reverse transcriptase PCR (qRT-PCR). Our results indicated that many genes in module 17 were upregulated during the heat shock and recovery processes and downregulated in response to low temperature. Furthermore, two putative genes, Vit_07s0185g00040 and Vit_02s0025g04060, were highly expressed in response to heat shock and recovery. This study provides insight into GGCN gene modules and offers important references for gene functions and the discovery of new genes at the module level.

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A new look at water transport regulation in plants - New Phytologist

A new look at water transport regulation in plants - New Phytologist | Plant Gene Seeker -PGS | Scoop.it
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SummaryPlant function requires effective mechanisms to regulate water transport at a variety of scales. Here, we develop a new theoretical framework describing plant responses to drying soil, based on the relationship between midday and predawn leaf water potentials. The intercept of the relationship (Λ) characterizes the maximum transpiration rate per unit of hydraulic transport capacity, whereas the slope (σ) measures the relative sensitivity of the transpiration rate and plant hydraulic conductance to declining water availability.This framework was applied to a newly compiled global database of leaf water potentials to estimate the values of Λ and σ for 102 plant species.Our results show that our characterization of drought responses is largely consistent within species, and that the parameters Λ and σ show meaningful associations with climate across species. Parameter σ was ≤1 in most species, indicating a tight coordination between the gas and liquid phases of water transport, in which canopy transpiration tended to decline faster than hydraulic conductance during drought, thus reducing the pressure drop through the plant.The quantitative framework presented here offers a new way of characterizing water transport regulation in plants that can be used to assess their vulnerability to drought under current and future climatic conditions.
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Understanding sustainable diets

Understanding sustainable diets | Plant Gene Seeker -PGS | Scoop.it

Four papers, three published in high impact peer-reviewed journals, further our understanding of sustainable diets.


Via Luigi Guarino
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AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis - New Phytologist

AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis - New Phytologist | Plant Gene Seeker -PGS | Scoop.it
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SummaryPlant root system plasticity is critical for survival in changing environmental conditions. One important aspect of root architecture is lateral root development, a complex process regulated by hormone, environmental and protein signalling pathways.Here we show, using molecular genetic approaches, that the MYB transcription factor AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis.We identify AtMYB93 as an interaction partner of the lateral-root-promoting ARABIDILLO proteins. Atmyb93 mutants have faster lateral root developmental progression and enhanced lateral root densities, while AtMYB93-overexpressing lines display the opposite phenotype. AtMYB93 is expressed strongly, specifically and transiently in the endodermal cells overlying early lateral root primordia and is additionally induced by auxin in the basal meristem of the primary root. Furthermore, Atmyb93 mutant lateral root development is insensitive to auxin, indicating that AtMYB93 is required for normal auxin responses during lateral root development.We propose that AtMYB93 is part of a novel auxin-induced negative feedback loop stimulated in a select few endodermal cells early during lateral root development, ensuring that lateral roots only develop when absolutely required. Putative AtMYB93 homologues are detected throughout flowering plants and represent promising targets for manipulating root systems in diverse crop species.
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Licensing MLH1 sites for crossover during meiosis | Nature Communications

Licensing MLH1 sites for crossover during meiosis | Nature Communications | Plant Gene Seeker -PGS | Scoop.it
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During meiosis, homologous chromosomes synapse and recombine at sites marked by the binding of the mismatch repair protein MLH1. In hexaploid wheat, the Ph1 locus has a major effect on whether crossover occurs between homologues or between related homoeologues. Here we report that—in wheat–rye hybrids where homologues are absent—Ph1 affects neither the level of synapsis nor the number of MLH1. Thus in the case of wheat–wild relative hybrids, Ph1 must affect whether MLH1 sites are able to progress to crossover. The observed level of synapsis implies that Ph1 functions to promote homologue pairing rather than suppress homoeologue pairing in wheat. Therefore, Ph1stabilises polyploidy in wheat by both promoting homologue pairing and preventing MLH1 sites from becoming crossovers on paired homoeologues during meiosis.


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Photosynthesis in a climate change scenario | Plant Science

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PREFACE

This Special Issue takes in consideration the importance of climate change and of photosynthesis as the life process most affected by global environmental changes. The issue contains a series of papers that address some of the most important recent advances in our understanding of how plant photosynthesis is regulated by the most important drivers of climate change. Hence, several papers (e.g. Cabot et al.; Gonzalez-Meler et al., Irigoyen et al.; Morales et al.) describe revisions of the most important methodologies employed for experimentally simulating climate change scenarios, and the key conclusions that have been derived from such studies over the past decades. Other papers consider, from either theoretical or experimental approaches, several important physiological aspects to be considered when addressing studies on plant responses to climate change including mesophyll conductance to CO2 (Flexas et al., Sun et al. a), Rubisco (Galmes et al.), carbon isotope discrimination (Perez-Lopez et al.), isoprene emission (Centritto et al.), monoubiquitin expression (Tian et al. a), foliar decreases (Ogaya et al.) or water use efficiency (Gago et al.). Finally, other papers present novel data on experimental approaches for understanding species specific photosynthetic responses to components of climate change such as elevated CO2, ozone and temperature (Ayub et al., Bunce; Rosenthal et al.; Sun et al. b; Wang and Heckathorn; Zang et al. a,b).

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Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines - The Plant Journal

Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines - The Plant Journal | Plant Gene Seeker -PGS | Scoop.it
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Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.


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The S-Domain Receptor Kinase Arabidopsis Receptor Kinase2 and the U Box/Armadillo Repeat-Containing E3 Ubiquitin Ligase9 Module Mediates Lateral Root Development under Phosphate Starvation in Arabi...

Andres Zurita's insight:

When plants encounter nutrient-limiting conditions in the soil, the root architecture is redesigned to generate numerous lateral roots (LRs) that increase the surface area of roots, promoting efficient uptake of these deficient nutrients. Of the many essential nutrients, reduced availability of inorganic phosphate has a major impact on plant growth because of the requirement of inorganic phosphate for synthesis of organic molecules, such as nucleic acids, ATP, and phospholipids, that function in various crucial metabolic activities. In our screens to identify a potential role for the S-domain receptor kinase1-6 and its interacting downstream signaling partner, the Arabidopsis (Arabidopsis thaliana) plant U box/armadillo repeat-containing E3 ligase9 (AtPUB9), we identified a role for this module in regulating LR development under phosphate-starved conditions. Our results show that Arabidopsis double mutant plants lackingAtPUB9 and Arabidopsis Receptor Kinase2 (AtARK2; ark2-1/pub9-1) display severely reduced LRs when grown under phosphate-starved conditions. Under these starvation conditions, these plants accumulated very low to no auxin in their primary root and LR tips as observed through expression of the auxin reporter DR5::uidA transgene. Exogenous auxin was sufficient to rescue the LRdevelopmental defects in the ark2-1/pub9-1 lines, indicating a requirement of auxin accumulation for this process. Our subcellular localization studies with tobacco (Nicotiana tabacum) suspension-cultured cells indicate that interaction between ARK2 and AtPUB9 results in accumulation of AtPUB9 in the autophagosomes. Inhibition of autophagy in wild-type plants resulted in reduction of LR development and auxin accumulation under phosphate-starved conditions, suggesting a role for autophagy in regulating LR development. Thus, our study has uncovered a previously unknown signaling module (ARK2-PUB9) that is required for auxin-mediated LR development under phosphate-starved conditions.


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Generation of Marker-free Transgenic Plants Concurrently Resistant to a DNA Geminivirus and a RNA Tospovirus | Scientific Reports

Generation of Marker-free Transgenic Plants Concurrently Resistant to a DNA Geminivirus and a RNA Tospovirus | Scientific Reports | Plant Gene Seeker -PGS | Scoop.it
Global threats of ssDNA geminivirus and ss(-)RNA tospovirus on crops necessitate the development of transgenic resistance. Here, we constructed a two-T DNA vector carrying a hairpin of the intergenic region (IGR) of Ageratum yellow vein virus (AYVV), residing in an intron inserted in an untranslatable nucleocapsid protein (NP) fragment of Melon yellow spot virus (MYSV). Transgenic tobacco lines highly resistant to AYVV and MYSV were generated. Accumulation of 24-nt siRNA, higher methylation levels on the IGR promoters of the transgene, and suppression of IGR promoter activity of invading AYVV indicate that AYVV resistance is mediated by transcriptional gene silencing. Lack of NP transcript and accumulation of corresponding siRNAs indicate that MYSV resistance is mediated through post-transcriptional gene silencing. Marker-free progenies with concurrent resistance to both AYVV and MYSV, stably inherited as dominant nuclear traits, were obtained. Hence, we provide a novel way for concurrent control of noxious DNA and RNA viruses with less biosafety concerns.
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Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing : Nature Communications : Nature Publishing Group

Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing : Nature Communications : Nature Publishing Group | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.

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Explaining the decrease in the genetic diversity of wheat in France over the 20th century

Explaining the decrease in the genetic diversity of wheat in France over the 20th century | Plant Gene Seeker -PGS | Scoop.it
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Highlights• We used a new integrative indicator to assess wheat genetic diversity in fields.• We studied the trend of wheat diversity in French landscapes in the 20th century.• Unlike the number of variety the index revealed increasing genetic homogenization.• The reasons are: landrace extinction, spatial homogenization, genetic similarity.• Genetic homogeneity might increase vulnerability and lower resilience of farming.
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Natural products from resurrection plants: Potential for medical applications

Natural products from resurrection plants: Potential for medical applications | Plant Gene Seeker -PGS | Scoop.it
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Resurrection species are a group of land plants that can tolerate extreme desiccation of their vegetative tissues during harsh drought stress, and still quickly – often within hours – regain normal physiological and metabolic functions following rehydration. At the molecular level, this desiccation tolerance is attributed to basal cellular mechanisms including the constitutive expression of stress-associated genes and high levels of protective metabolites present already in the absence of stress, as well as to transcriptome and metabolome reconfigurations rapidly occurring during the initial phases of drought stress. Parts of this response are conferred by unique metabolites, including a diverse array of sugars, phenolic compounds, and polyols, some of which accumulate to high concentrations within the plant cell. In addition to drought stress, these metabolites are proposed to contribute to the protection against other abiotic stresses and to an increased oxidative stress tolerance. Recently, extracts of resurrection species and particular secondary metabolites therein were reported to display biological activities of importance to medicine, with e.g. antibacterial, anticancer, antifungal, and antiviral activities, rendering them possible candidates for the development of novel drug substances as well as for cosmetics. Herein, we provide an overview of the metabolite composition of resurrection species, summarize the latest reports related to the use of natural products from resurrection plants, and outline their potential for medical applications.


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The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication : Nature Genetics

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication : Nature Genetics | Plant Gene Seeker -PGS | Scoop.it
Mingsheng Chen, Klaus Mayer, Steve Rounsley, Rod Wing and colleagues report the genome sequence of African rice (Oryza glaberrima), a different species than Asian rice. The authors resequenced 20 O. glaberrima accessions and 94 Oryza barthii accessions (the putative progenitor species of O. glaberrima), and their analyses support the hypothesis that O. glaberrima was domesticated in a single region along the upper Niger river.
Andres Zurita's insight:

The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrimagenome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis thatO. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

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Transport of Boron by the tassel-less1 Aquaporin Is Critical for Vegetative and Reproductive Development in Maize

Transport of Boron by the tassel-less1 Aquaporin Is Critical for Vegetative and Reproductive Development in Maize | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The element boron (B) is an essential plant micronutrient, and B deficiency results in significant crop losses worldwide. The maize (Zea mays) tassel-less1 (tls1) mutant has defects in vegetative and inflorescence development, comparable to the effects of B deficiency. Positional cloning revealed that tls1 encodes a protein in the aquaporin family co-orthologous to known B channel proteins in other species. Transport assays show that the TLS1 protein facilitates the movement of B and water into Xenopus laevis oocytes. B content is reduced in tls1 mutants, and application of B rescues the mutant phenotype, indicating that the TLS1 protein facilitates the movement of B in planta. B is required to cross-link the pectic polysaccharide rhamnogalacturonan II (RG-II) in the cell wall, and the percentage of RG-II dimers is reduced in tls1 inflorescences, indicating that the defects may result from altered cell wall properties. Plants heterozygous for bothtls1 and rotten ear (rte), the proposed B efflux transporter, exhibit a dosage-dependent defect in inflorescence development under B-limited conditions, indicating that both TLS1 and RTE function in the same biological processes. Together, our data provide evidence that TLS1 is a B transport facilitator in maize, highlighting the importance of B homeostasis in meristem function.


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PLETHORA gradient formation mechanism separates auxin responses

PLETHORA gradient formation mechanism separates auxin responses | Plant Gene Seeker -PGS | Scoop.it

During plant growth, dividing cells in meristems must coordinate transitions from division to expansion and differentiation, thus generating three distinct developmental zones: the meristem, elongation zone and differentiation zone1. Simultaneously, plants display tropisms, rapid adjustments of their direction of growth to adapt to environmental conditions. It is unclear how stable zonation is maintained during transient adjustments in growth direction. In Arabidopsis roots, many aspects of zonation are controlled by the phytohormone auxin and auxin-induced PLETHORA (PLT) transcription factors, both of which display a graded distribution with a maximum near the root tip2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. In addition, auxin is also pivotal for tropic responses13, 14. Here, using an iterative experimental and computational approach, we show how an interplay between auxin and PLTs controls zonation and gravitropism. We find that the PLT gradient is not a direct, proportionate readout of the auxin gradient. Rather, prolonged high auxin levels generate a narrow PLT transcription domain from which a gradient of PLT protein is subsequently generated through slow growth dilution and cell-to-cell movement. The resulting PLT levels define the location of developmental zones. In addition to slowly promoting PLT transcription, auxin also rapidly influences division, expansion and differentiation rates. We demonstrate how this specific regulatory design in which auxin cooperates with PLTs through different mechanisms and on different timescales enables both the fast tropic environmental responses and stable zonation dynamics necessary for coordinated cell differentiation.


Via Christophe Jacquet
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Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

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Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa andB. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

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Proline-rich protein-like PRPL1 controls elongation of root hairs in Arabidopsis thaliana

Proline-rich protein-like PRPL1 controls elongation of root hairs in Arabidopsis thaliana | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

The synthesis and composition of cell walls is dynamically adapted in response to many developmental and environmental signals. In this respect, cell wall proteins involved in controlling cell elongation are critical for cell development. Transcriptome analysis identified a gene inArabidopsis thaliana, which was named proline-rich protein-like, AtPRPL1, based on sequence similarities from a phylogenetic analysis. The most resemblance was found to AtPRP1 and AtPRP3 from Arabidopsis, which are known to be involved in root hair growth and development. In A. thalianafour proline-rich cell wall protein genes, playing a role in building up the cross-connections between cell wall components, can be distinguished.AtPRPL1 is a small gene that in promoter::GUS (β-glucuronidase) analysis has high expression in trichoblast cells and in the collet. Chemical or mutational interference with root hair formation inhibited this expression. Altered expression levels in knock-out or overexpression lines interfered with normal root hair growth and etiolated hypocotyl development, but Fourier transform-infrared (FT-IR) analysis did not identify consistent changes in cell wall composition of root hairs and hypocotyl. Co-localization analysis of the AtPRPL1–green fluorescent protein (GFP) fusion protein and different red fluorescent protein (RFP)-labelled markers confirmed the presence of AtPRPL1–GFP in small vesicles moving over the endoplasmic reticulum. Together, these data indicate that the AtPRPL1 protein is involved in the cell’s elongation process. How exactly this is achieved remains unclear at present.

 
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Tandem CCCH Zinc Finger Proteins in Plant Growth, Development and Stress Response

Tandem CCCH Zinc Finger Proteins in Plant Growth, Development and Stress Response | Plant Gene Seeker -PGS | Scoop.it
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Cysteine3Histidine (CCCH)-type zinc finger proteins comprise a large family that is well conserved across eukaryotes. Among them, tandem CCCH zinc finger proteins (TZFs) play critical roles in mRNA metabolism in animals and yeast. While there are only three TZF members in humans, a much higher number of TZFs has been found in many plant species. Notably, plant TZFs are over-represented by a class of proteins containing a unique TZF domain preceded by an arginine (R)-rich (RR) motif, hereafter called RR-TZF. Recently, there have been a large number of reports indicating that RR-TZF proteins can localize to processing bodies (P-bodies) and stress granules (SG), two novel cytoplasmic aggregations of messenger ribonucleoprotein complexes (mRNPs), and play critical roles in plant growth, development and stress response, probably via RNA regulation. This review focuses on the classification and most recent development of molecular, cellular and genetic analyses of plant RR-TZF proteins.

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Molecular genetic framework for protophloem formation

Molecular genetic framework for protophloem formation | Plant Gene Seeker -PGS | Scoop.it
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Significance

The emergence of vascular tissues played a central role in the plant conquest of land. Both xylem and phloem are essential for the development of flowering plants, yet little is known about the molecular genetic control of phloem specification and differentiation. Here we show that delicate quantitative interplay between two opposing signaling pathways determines cellular commitment to protophloem sieve element fate in root meristems of the model plant Arabidopsis thaliana. Our data suggest that a recently described phloem-specific protein is a positive, quantitative master regulator of phloem fate.

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The genome of the stress-tolerant wild tomato species Solanum pennellii | Nature Genetics

The genome of the stress-tolerant wild tomato species Solanum pennellii | Nature Genetics | Plant Gene Seeker -PGS | Scoop.it
Bjorn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii. The authors identify genes important for stress tolerance, metabolism and fruit maturation and suggest that transposable elements have had an important role in the evolution of the S. penellii stress response.
Andres Zurita's insight:

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicumare replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.


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Chile needs better science governance and support

Chile needs better science governance and support | Plant Gene Seeker -PGS | Scoop.it
Its scientists have much to offer the world, but are being held back by scattered administration and changing policies, argues Pablo Astudillo Besnier.
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Yet, despite the glossy images of the telescopes promising a high-tech future, in 2012, Chile spent just 0.35% of its gross domestic product on research and development (R&D) — the least of all countries in the Organisation for Economic Co-operation and Development. Two-thirds of the academic publications come from just five universities. And, perhaps most importantly, a heavy focus on applied science threatens to stifle basic research and its potential to innovate.

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Slicing the wheat genome

Slicing the wheat genome | Plant Gene Seeker -PGS | Scoop.it
Andres Zurita's insight:

This year celebrates the 100th anniversary of the birth of Norman Borlaug, the Nobel Prize-winning plant geneticist who, through his contribution to the “green revolution,” reminds us of the importance of applying scientific knowledge to develop crop varieties. This is even more important today as we face a rapidly expanding global population, climate change, and the need to keep agricultural efforts sustainable while minimizing environmental impacts. Accessing the fundamental information of crop genomes aids in accelerating breeding pipelines and improves our understanding of the molecular basis of agronomically important traits, such as yield and tolerance to abiotic and biotic stresses.

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