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Transcriptomic analysis of grape (Vitis vinifera L.) leaves during and after recovery from heat stress

Background

Grapes are a major fruit crop around the world. Heat stress can significantly reduce grape yield and quality. Changes at the molecular level in response to heat stress and subsequent recovery are poorly understood. To elucidate the effect of heat stress and subsequent recovery on expression of genes by grape leaves representing the classic heat stress response and thermotolerance mechanisms, transcript abundance of grape (Vitis vinifera L.) leaves was quantified using the Affymetrix Grape Genome oligonucleotide microarray (15,700 transcripts), followed by quantitative Real-Time PCR validation for some transcript profiles.

Results

We found that about 8% of the total probe sets were responsive to heat stress and/or to subsequent recovery in grape leaves. The heat stress and recovery responses were characterized by different transcriptional changes. The number of heat stress-regulated genes was almost twice the number of recovery-regulated genes. The responsive genes identified in this study belong to a large number of important traits and biological pathways, including cell rescue (i.e., antioxidant enzymes), protein fate (i.e., HSPs), primary and secondary metabolism, transcription factors, signal transduction, and development. We have identified some common genes and heat shock factors (HSFs) that were modulated differentially by heat stress and recovery. Most HSP genes were upregulated by heat stress but were downregulated by the recovery. On the other hand, some specific HSP genes or HSFs were uniquely responsive to heat stress or recovery.

Conclusion

The effect of heat stress and recovery on grape appears to be associated with multiple processes and mechanisms including stress-related genes, transcription factors, and metabolism. Heat stress and recovery elicited common up- or downregulated genes as well as unique sets of responsive genes. Moreover, some genes were regulated in opposite directions by heat stress and recovery. The results indicated HSPs, especially small HSPs, antioxidant enzymes (i.e., ascorbate peroxidase), and galactinol synthase may be important to thermotolerance of grape. HSF30 may be a key regulator for heat stress and recovery, while HSF7 and HSF1 may only be specific to recovery. The identification of heat stress or recovery responsive genes in this study provides novel insights into the molecular basis for heat tolerance in grape leaves.

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Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes

Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, all of these functions can tolerate some sequence variation, not explaining their ultraconserved and ultraselected nature. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ~115 Mya. We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like Elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ~50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.

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Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana

Background

Silicon plays important biological roles, but the mechanisms of cellular responses to silicon are poorly understood. We report the first analysis of cell cycle arrest and recovery from silicon starvation in the diatom Thalassiosira pseudonana using whole genome microarrays.

Results

Three known responses to silicon were examined, 1) silicified cell wall synthesis, 2) recovery from silicon starvation, and 3) co-regulation with silicon transporter (SIT) genes. In terms of diatom cell wall formation, thus far only cell surface proteins and proteins tightly associated with silica have been characterized. Our analysis has identified new genes potentially involved in silica formation, and other genes potentially involved in signaling, trafficking, protein degradation, glycosylation and transport, which provides a larger-scale picture of the processes involved. During silicon starvation, an overrepresentation of transcription and translation related genes were up-regulated, indicating that T. pseudonana is poised to rapidly recover from silicon starvation and resume cell cycle progression upon silicon replenishment. This is in contrast to other types of limitation, and provides the first molecular data explaining the well-established environmental response of diatoms to grow as blooms and to out-compete other classes of microalgae for growth. Comparison of our data with a previous diatom cell cycle analysis indicates that assignment of the cell cycle specific stage of particular cyclins and cyclin dependent kinases should be re-evaluated. Finally, genes co-varying in expression with the SITs enabled identification of a new class of diatom-specific proteins containing a unique domain, and a putative silicon efflux protein.

Conclusions

Analysis of the T. pseudonana microarray data has provided a wealth of new genes to investigate previously uncharacterized cellular phenomenon related to silicon metabolism, silicon's interaction with cellular components, and environmental responses to silicon.

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Proteomic analysis of rice leaves during drought ... [Proteomics. 2002] - PubMed - NCBI

Three-week old plants of rice (Oryza sativa L. cv CT9993 and cv IR62266) developed gradual water stress over 23 days of transpiration without watering, during which period the mid-day leaf water potential declined to approximately -2.4 MPa, compared with approximately -1.0 MPa in well-watered controls. More than 1000 protein spots that were detected in leaf extracts by proteomic analysis showed reproducible abundance within replications. Of these proteins, 42 spots showed a significant change in abundance under stress, with 27 of them exhibiting a different response pattern in the two cultivars. However, only one protein (chloroplast Cu-Zn superoxide dismutase) changed significantly in opposite directions in the two cultivars in response to drought. The most common difference was for proteins to be up-regulated by drought in CT9993 and unaffected in IR62266; or down-regulated by drought in IR62266 and unaffected in CT9993. By 10 days after rewatering, all proteins had returned completely or largely to the abundance of the well-watered control. Mass spectrometry helped to identify 16 of the drought-responsive proteins, including an actin depolymerizing factor, which was one of three proteins detectable under stress in both cultivars but undetectable in well-watered plants or in plants 10 days after rewatering. The most abundant protein up-regulated by drought in CT9993 and IR62266 was identified only after cloning of the corresponding cDNA. It was found to be an S-like RNase homologue but it lacked the two active site histidines required for RNase activity. Four novel drought-responsive mechanisms were revealed by this work: up-regulation of S-like RNase homologue, actin depolymerizing factor and rubisco activase, and down-regulation of isoflavone reductase-like protein.
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Proteomic analysis of rice leaf, stem and root ti... [Proteomics. 2006] - PubMed - NCBI

PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat

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SHARSHERET, Israel: A Breakthrough In Agricultural Biotechnology –Trait Delivery Innovator Morflora Accelerates Gene Delivery Process in Seeds | Business Wire | Rock Hill Herald Online

SHARSHERET, Israel: A Breakthrough In Agricultural Biotechnology –Trait Delivery Innovator Morflora Accelerates Gene Delivery Process in Seeds | Business Wire | Rock Hill Herald Online | Plant Genomics | Scoop.it
Morflora ( www.morflora.com ), focused on innovative non-transgenic trait delivery technology for plant protection reports today that its TraitUP™ platform has been successfully used to deliver complex genetic material into seeds, providing...
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Computational Biology in the 21st Century: Making Sense out of Massive Data

Computational Biology in the 21st Century: Making Sense out of Massive Data Air date: Wednesday, February 01, 2012, 3:00:00 PMCategory: Wednesday Afternoon Lectures Description: The last two decades have seen an exponential increase in genomic and...
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Trends in Plant Science - A survey of dominant mutations in Arabidopsis thaliana

Following the recent publication of a comprehensive dataset of 2400 genes with a loss-of-function mutant phenotype in Arabidopsis (Arabidopsis thaliana), questions remain concerning the diversity of dominant mutations in Arabidopsis. Most of these dominant phenotypes are expected to result from inappropriate gene expression, novel protein function, or disrupted protein complexes. This review highlights the major classes of dominant mutations observed in model organisms and presents a collection of 200 Arabidopsis genes associated with a dominant or semidominant phenotype. Emphasis is placed on mutants identified through forward genetic screens of mutagenized or activation-tagged populations. These datasets illustrate the variety of genetic changes and protein functions that underlie dominance in Arabidopsis and may ultimately contribute to phenotypic variation in flowering plants.

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Alam does it again - Daily Star Online

Alam does it again - Daily Star Online | Plant Genomics | Scoop.it
Alam does it againDaily Star OnlineGenome sequencing helps scientists find genes much more easily and quickly.
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Whole transcriptome analysis of the silicon response of the diatom ... - 7thSpace Interactive (press release)

Whole transcriptome analysis of the silicon response of the diatom ...7thSpace Interactive (press release)Silicon plays important biological roles, but the mechanisms of cellular responses to silicon are poorly understood.
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Sequencing fungus genome: A nonpareil achievement - Financial Express Bangladesh

Sequencing fungus genome: A nonpareil achievement - Financial Express Bangladesh | Plant Genomics | Scoop.it
Sequencing fungus genome: A nonpareil achievementFinancial Express BangladeshHowever, the benefit of the mapping of the fungus' building block will cover 500 plants in total because all such plants are attacked by this fungus.
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Why Assembling Plant Genome Sequences Is So Challenging

Abstract:

In spite of the biological and economic importance of plants, relatively few plant species have been sequenced. Only the genome sequence of plants with relatively small genomes, most of them angiosperms, in particular eudicots, has been determined. The arrival of next-generation sequencing technologies has allowed the rapid and efficient development of new genomic resources for non-model or orphan plant species. But the sequencing pace of plants is far from that of animals and microorganisms. This review focuses on the typical challenges of plant genomes that can explain why plant genomics is less developed than animal genomics. Explanations about the impact of some confounding factors emerging from the nature of plant genomes are given. As a result of these challenges and confounding factors, the correct assembly and annotation of plant genomes is hindered, genome drafts are produced, and advances in plant genomics are delayed.

Keywords:

plant sequencing; NGS; complexity; repeats; assemblers; polyploidy; bioinformatics

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PLOS ONE: Whole Genome Duplication Affects Evolvability of Flowering Time in an Autotetraploid Plant

PLOS ONE: Whole Genome Duplication Affects Evolvability of Flowering Time in an Autotetraploid Plant | Plant Genomics | Scoop.it

Whole genome duplications have occurred recurrently throughout the evolutionary history of eukaryotes. The resulting genetic and phenotypic changes can influence physiological and ecological responses to the environment; however, the impact of genome copy number on evolvability has rarely been examined experimentally. Here, we evaluate the effect of genome duplication on the ability to respond to selection for early flowering time in lines drawn from naturally occurring diploid and autotetraploid populations of the plant Chamerion angustifolium (fireweed). We contrast this with the result of four generations of selection on synthesized neoautotetraploids, whose genic variability is similar to diploids but genome copy number is similar to autotetraploids. In addition, we examine correlated responses to selection in all three groups. Diploid and both extant tetraploid and neoautotetraploid lines responded to selection with significant reductions in time to flowering. Evolvability, measured as realized heritability, was significantly lower in extant tetraploids ( = 0.31) than diploids ( = 0.40). Neotetraploids exhibited the highest evolutionary response ( = 0.55). The rapid shift in flowering time in neotetraploids was associated with an increase in phenotypic variability across generations, but not with change in genome size or phenotypic correlations among traits. Our results suggest that whole genome duplications, without hybridization, may initially alter evolutionary rate, and that the dynamic nature of neoautopolyploids may contribute to the prevalence of polyploidy throughout eukaryotes.

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Pollen cells keep memory to control jumping genes

Pollen cells keep memory to control jumping genes | Plant Genomics | Scoop.it
Using the plant model Arabidopsis thaliana, Jörg Becker, José Feijó and their team, at the IGC, and Robert Martienssen and colleagues, at CSHL, analysed the genome of pollen grains and their precursor cells, the ...
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Chinese scientists successfully crack the genome of diploid cotton

Chinese scientists successfully crack the genome of diploid cotton | Plant Genomics | Scoop.it
Through the phylogenetic analysis on G. raimondii and eight other sequenced plant genomes, they found that the cotton, and probably Theobroma cacao, were the only sequenced plant species that possess an authentic ...
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Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species

Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species | Plant Genomics | Scoop.it

Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

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Plant B Vitamin Pathways and their Compartmentation: a Guide for the Perplexed

Plant B Vitamin Pathways and their Compartmentation: a Guide for the Perplexed | Plant Genomics | Scoop.it

The B vitamins and the cofactors derived from them are essential for life. B vitamin synthesis in plants is consequently as crucial to plants themselves as it is to humans and animals, whose B vitamin nutrition depends largely on plants. The synthesis and salvage pathways for the seven plant B vitamins are now broadly known, but certain enzymes and many transporters have yet to be identified, and the subcellular locations of various reactions are unclear. Although very substantial, what is not known about plant B vitamin pathways is regrettably difficult to discern from the literature or from biochemical pathway databases. Nor do databases accurately represent all that is known about B vitamin pathways—above all their compartmentation—because the facts are scattered throughout the literature, and thus hard to piece together. These problems (i) deter discoveries because newcomers to B vitamins cannot see which mysteries still need solving; and (ii) impede metabolic reconstruction and modelling of B vitamin pathways because genes for reactions or transport steps are missing. This review therefore takes a fresh approach to capture current knowledge of B vitamin pathways in plants. The synthesis pathways, key salvage routes, and their subcellular compartmentation are surveyed in depth, and encoded in the SEED database (http://pubseed.theseed.org/seedviewer.cgi?page=PlantGateway) for Arabidopsis and maize. The review itself and the encoded pathways specifically identify enigmatic or missing reactions, enzymes, and transporters. The SEED-encoded B vitamin pathway collection is a publicly available, expertly curated, one-stop resource for metabolic reconstruction and modeling.

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Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat - up-to-the-minute news and headlines. 7thSpace is a online portal covering topics such as Family, Business, Entertainment, Headlines, Recipes and more.
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High-throughput sequencing of black pepper root transcriptome - 7thSpace Interactive (press release)

High-throughput sequencing of black pepper root transcriptome7thSpace Interactive (press release)Results: The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method.
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NSF awards $10M for crop genome data resources

NSF awards $10M for crop genome data resources | Plant Genomics | Scoop.it
Cold Spring Harbor Laboratory and Oregon State University have been awarded $10m by the National Science Foundation (NSF) to fund the development publically available genomic data resources for crop plants including ...
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BD scientists crack genome sequencing of fungal pathogen - Financial Express Bangladesh

BD scientists crack genome sequencing of fungal pathogen - Financial Express Bangladesh | Plant Genomics | Scoop.it
BD scientists crack genome sequencing of fungal pathogenFinancial Express BangladeshPrime Minister Sheikh Hasina Wednesday announced in the Parliament that a group of Bangladeshi scientists have decoded the genome sequencing of a fungal pathogen...
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Growing better poplars for biofuels - Phys.Org

Growing better poplars for biofuels - Phys.Org | Plant Genomics | Scoop.it
Growing better poplars for biofuelsPhys.OrgSo Busov is using some 21st century tools—the genome of the poplar tree and snippets of DNA known as activation tags—to identify the genes that make plants grow faster or change their chemical or physical...
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