Plant Genomics
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Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (fagus grandifolia)

Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests.
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Abstract (provisional)Background

Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests. The disease begins when exotic beech scale insects feed on the bark of trees, and is followed by infection of damaged bark tissues by native or exotic fungi. Proteomic analysis was conducted of beech bark proteins from diseased trees and healthy trees in areas heavily infested with beech bark disease. All of the diseased trees had signs of Neonectria infection such as cankers or fruiting bodies. In previous tests reported elsewhere, all of the diseased trees were demonstrated to be susceptible to the scale insect and all of the healthy trees were demonstrated to be resistant to the scale insect. Sixteen trees were sampled from eight geographically isolated stands, the sample consisting of 10 healthy (scale-resistant) and 6 diseased/infested (scale-susceptible) trees.

Results

Proteins were extracted from each tree and analysed in triplicate by isoelectric focusing followed by denaturing gel electrophoresis. Gels were stained and protein spots identified and intensity quantified, then a statistical model was fit to identify significant differences between trees. A subset of BBD differential proteins were analysed by mass spectrometry and matched to known protein sequences for identification. Identified proteins had homology to stress, insect, and pathogen related proteins in other plant systems. Protein spots significantly different in diseased and healthy trees having no stand or disease-by-stand interaction effects were identified.

Conclusions

Further study of these proteins should help to understand processes critical to resistance to beech bark disease and to develop biomarkers for use in tree breeding programs and for the selection of resistant trees prior to or in early stages of BBD development in stands. Early identification of resistant trees (prior to the full disease development in an area) will allow forest management through the removal of susceptible trees and their root-sprouts prior to the onset of disease, allowing management and mitigation of costs, economic impact, and impacts on ecological systems and services.

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Transcriptome analysis of bitter acid biosynthesis and precursor pathways in hop (Humulus lupulus)

Bitter acids (e.g. humulone) are prenylated polyketides synthesized in lupulin glands of the hop plant (Humulus lupulus) which are important contributors to the bitter flavour and stability of beer.
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Abstract (provisional)Background

Bitter acids (e.g. humulone) are prenylated polyketides synthesized in lupulin glands of the hop plant (Humulus lupulus) which are important contributors to the bitter flavour and stability of beer. Bitter acids are formed from acyl-CoA precursors derived from branched-chain amino acid (BCAA) degradation and C5 prenyl diphosphates from the methyl-D-erythritol 4-phosphate (MEP) pathway. We used RNA sequencing (RNA-seq) to obtain the transcriptomes of isolated lupulin glands, cones with glands removed and leaves from high alpha-acid hop cultivars, and analyzed these datasets for genes involved in bitter acid biosynthesis including the supply of major precursors. We also measured the levels of BCAAs, acyl-CoA intermediates, and bitter acids in glands, cones and leaves.

Results

Transcripts encoding all the enzymes of BCAA metabolism were significantly more abundant in lupulin glands, indicating that BCAA biosynthesis and subsequent degradation occurs in these specialized cells. Branched-chain acyl-CoAs and bitter acids were present at higher levels in glands compared with leaves and cones. RNA-seq analysis showed the gland-specific expression of the MEP pathway, enzymes of sucrose degradation and several transcription factors that may regulate bitter acid biosynthesis in glands. Two branched-chain aminotransferase (BCAT) enzymes, HlBCAT1 and HlBCAT2, were abundant, with gene expression quantification by RNA-seq and qRT-PCR indicating that HlBCAT1 was specific to glands while HlBCAT2 was present in glands, cones and leaves. Recombinant HlBCAT1 and HlBCAT2 catalyzed forward (biosynthetic) and reverse (catabolic) reactions with similar kinetic parameters. HlBCAT1 is targeted to mitochondria where it likely plays a role in BCAA catabolism. HlBCAT2 is a plastidial enzyme likely involved in BCAA biosynthesis. Phylogenetic analysis of the hop BCATs and those from other plants showed that they group into distinct biosynthetic (plastidial) and catabolic (mitochondrial) clades.

Conclusions

Our analysis of the hop transcriptome significantly expands the genomic resources available for this agriculturally-important crop. This study provides evidence for the lupulin gland-specific biosynthesis of BCAAs and prenyl diphosphates to provide precursors for the production of bitter acids. The biosynthetic pathway leading to BCAAs in lupulin glands involves the plastidial enzyme, HlBCAT2. The mitochondrial enzyme HlBCAT1 degrades BCAAs as the first step in the catabolic pathway leading to branched chain-acyl-CoAs.

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Transcriptome Analysis of Cytokinin Response in Tomato Leaves

Transcriptome Analysis of Cytokinin Response in Tomato Leaves | Plant Genomics | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
Biswapriya Biswavas Misra's insight:
Abstract

Tomato is one of the most economically and agriculturally important Solanaceous species and vegetable crops, serving as a model for examination of fruit biology and compound leaf development. Cytokinin is a plant hormone linked to the control of leaf development and is known to regulate a wide range of genes including many transcription factors. Currently there is little known of the leaf transcriptome in tomato and how it might be regulated by cytokinin. We employ high throughput mRNA sequencing technology and bioinformatic methodologies to robustly analyze cytokinin regulated tomato leaf transcriptomes. Leaf samples of two ages, 13d and 35d were treated with cytokinin or the solvent vehicle control dimethyl sulfoxide (DMSO) for 2 h or 24 h, after which RNA was extracted for sequencing. To confirm the accuracy of RNA sequencing results, we performed qPCR analysis of select transcripts identified as cytokinin regulated by the RNA sequencing approach. The resulting data provide the first hormone transcriptome analysis of leaves in tomato. Specifically we identified several previously untested tomato orthologs of cytokinin-related genes as well as numerous novel cytokinin-regulated transcripts in tomato leaves. Principal component analysis of the data indicates that length of cytokinin treatment and plant age are the major factors responsible for changes in transcripts observed in this study. Two hour cytokinin treatment showed a more robust transcript response indicated by both greater fold change of induced transcripts and the induction of twice as many cytokinin-related genes involved in signaling, metabolism, and transport in young vs. older leaves. This difference in transcriptome response in younger vs. older leaves was also found to a lesser extent with an extended (24 h) cytokinin treatment. Overall data presented here provides a solid foundation for future study of cytokinin and cytokinin regulated genes involved in compound leaf development or other developmental processes in tomato.

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Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to 'Candidatus Liberibacter asiaticus' infection

Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp. Several citrus GeneChip studies have revealed thousands of genes that are up- or down-regulated by infection with Ca. Liberibacter asiaticus. However, whether and how these host genes act to protect against HLB remains poorly understood.

Results

As a first step towards a mechanistic view of citrus in response to the HLB bacterial infection, we performed a comparative transcriptome analysis and found that a total of 21 Probesets are commonly up-regulated by the HLB bacterial infection. In addition, a number of genes are likely regulated specifically at early, late or very late stages of the infection. Furthermore, using Pearson correlation coefficient-based gene coexpression analysis, we constructed a citrus HLB response network consisting of 3,507 Probesets and 56,287 interactions. Genes involved in carbohydrate and nitrogen metabolic processes, transport, defense, signaling and hormone response were overrepresented in the HLB response network and the subnetworks for these processes were constructed. Analysis of the defense and hormone response subnetworks indicates that hormone response is interconnected with defense response. In addition, mapping the commonly up-regulated HLB responsive genes into the HLB response network resulted in a core subnetwork where transport plays a key role in the citrus response to the HLB bacterial infection. Moreover, analysis of a phloem protein subnetwork indicates a role for this protein and zinc transporter or zinc-binding proteins in the citrus HLB defense response.

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De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

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Abstract

Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation.

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Next Generation Sequencing in Predicting Gene Function in Podophyllotoxin Biosynthesis

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Abstract

Podophyllum species are sources of (−)-podophyllotoxin, an aryltetralin lignan used for semi-synthesis of various powerful and extensively employed cancer-treating drugs. Its biosynthetic pathway, however, remains largely unknown, with the last unequivocally demonstrated intermediate being (−)-matairesinol. Herein, massively parallel sequencing of Podophyllum hexandrum and Podophyllum peltatum transcriptomes and subsequent bioinformatics analyses of the corresponding assemblies were carried out. Validation of the assembly process was first achieved through confirmation of assembled sequences with those of various genes previously established as involved in podophyllotoxin biosynthesis as well as other candidate biosynthetic pathway genes. This contribution describes characterization of two of the latter, namely the cytochrome P450s, CYP719A23 from P. hexandrum and CYP719A24 from P. peltatum. Both enzymes were capable of converting (−)-matairesinol into (−)-pluviatolide by catalyzing methylenedioxy bridge formation and did not act on other possible substrates tested. Interestingly, the enzymes described herein were highly similar to methylenedioxy bridge-forming enzymes from alkaloid biosynthesis, whereas candidates more similar to lignan biosynthetic enzymes were catalytically inactive with the substrates employed. This overall strategy has thus enabled facile further identification of enzymes putatively involved in (−)-podophyllotoxin biosynthesis and underscores the deductive power of next generation sequencing and bioinformatics to probe and deduce medicinal plant biosynthetic pathways.

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BMC Bioinformatics | Full text | Computational prediction of novel non-coding RNAs in Arabidopsis thaliana

Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes.
Biswapriya Biswavas Misra's insight:
AbstractBackground

Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using tiling arrays in organisms such as human and Arabidopsis have revealed a great number of transcripts, a large portion of which have little or no capability to encode proteins. This unexpected finding suggests that the currently known repertoire of ncRNAs may only represent a small fraction of ncRNAs of the organisms. Thus, efficient and effective prediction of ncRNAs has become an important task in bioinformatics in recent years. Among the available computational methods, the comparative genomic approach seems to be the most powerful to detect ncRNAs. The recent completion of the sequencing of several major plant genomes has made the approach possible for plants.

Results

We have developed a pipeline to predict novel ncRNAs in the Arabidopsis (Arabidopsis thaliana) genome. It starts by comparing the expressed intergenic regions of Arabidopsis as provided in two whole-genome high-density oligo-probe arrays from the literature with the intergenic nucleotide sequences of all completely sequenced plant genomes including rice (Oryza sativa), poplar (Populus trichocarpa), grape (Vitis vinifera), and papaya (Carica papaya). By using multiple sequence alignment, a popular ncRNA prediction program (RNAz), wet-bench experimental validation, protein-coding potential analysis, and stringent screening against various ncRNA databases, the pipeline resulted in 16 families of novel ncRNAs (with a total of 21 ncRNAs).

Conclusion

In this paper, we undertake a genome-wide search for novel ncRNAs in the genome of Arabidopsis by a comparative genomics approach. The identified novel ncRNAs are evolutionarily conserved between Arabidopsis and other recently sequenced plants, and may conduct interesting novel biological functions.

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Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique - Online First - Springer

Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique - Online First - Springer | Plant Genomics | Scoop.it
Biswapriya Biswavas Misra's insight:
Abstract

The endosperm plays an important role in seed formation and germination, especially in rice (Oryza sativa). We used a high-throughput sequencing technique (RNA-Seq) to reveal the molecular mechanisms involved in rice endosperm development. Three cDNA libraries were taken from rice endosperm at 3, 6 and 10 days after pollination (DAP), which resulted in the detection of 21,596, 20,910 and 19,459 expressed gens, respectively. By ERANGE, we identified 10,371 differentially expressed genes (log2Ratio ≥1, FDR ≤0.001). The results were compared against three public databases (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and MapMan) in order to annotate the gene descriptions, associate them with gene ontology terms and to assign each to pathways. A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development. Interestingly, most metabolic pathways were down-regulated between 3 and 10 DAP except for those involved in the accumulation of material, such as starch/sucrose and protein metabolism. We also identified the expression of 1,118 putative transcription factor genes in endosperm development. The RNA-Seq results provide further systematic understanding of rice endosperm development at a fine scale and a foundation for future studies.

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Novel aspects of grapevine response to phytoplasma infection investigated by a proteomic and phospho-proteomic approach with data integration into functional networks

Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection. Among the latter, phosphorylation is critical in modulating protein structure, localization and interaction with other partners. In this work, we used a multiplex staining approach with 2D gels to study quantitative changes in the proteome and phosphoproteome of Flavescence doree-affected and recovered' Barbera' grapevines, compared to healthy plants.

Results

We identified 48 proteins that differentially changed in abundance, phosphorylation, or both in response to Flavescence doree phytoplasma infection. Most of them did not show any significant difference in recovered plants, which, by contrast, were characterized by changes in abundance, phosphorylation, or both for 17 proteins not detected in infected plants. Some enzymes involved in the antioxidant response that were up-regulated in infected plants, such as isocitrate dehydrogenase and glutathione S-transferase, returned to healthy-state levels in recovered plants. Others belonging to the same functional category were even down-regulated in recovered plants (oxidoreductase GLYR1 and ascorbate peroxidase). Our proteomic approach thus agreed with previously published biochemical and RT-qPCR data which reported down-regulation of scavenging enzymes and accumulation of H2O2 in recovered plants, possibly suggesting a role for this molecule in remission from infection. Fifteen differentially phosphorylated proteins (| ratio | > 2, p < 0.05) were identified in infected compared to healthy plants, including proteins involved in photosynthesis, response to stress and the antioxidant system. Many were not differentially phosphorylated in recovered compared to healthy plants, pointing to their specific role in responding to infection, followed by a return to a steady-state phosphorylation level after remission of symptoms. Gene ontology (GO) enrichment and statistical analysis showed that the general main category "response to stimulus" was over-represented in both infected and recovered plants but, in the latter, the specific child category "response to biotic stimulus" was no longer found, suggesting a return to steady-state levels for those proteins specifically required for defence against pathogens.

Conclusions

Proteomic data were integrated into biological networks and their interactions were represented through a hypothetical model, showing the effects of protein modulation on primary metabolic ways and related secondary pathways. By following a multiplex-staining approach, we obtained new data on grapevine proteome pathways that specifically change at the phosphorylation level during phytoplasma infection and following recovery, focusing for the first time on phosphoproteome changes during pathogen infection in this host.

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Journal of Biomedical Semantics | Abstract | OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists' toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment.

Results

We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy's capability for enriching, modifying and querying biomedical ontologies.

Conclusions

Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

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Andres Zurita's curator insight, January 17, 2013 6:38 AM
Background

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists' toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment.

Results

We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy's capability for enriching, modifying and querying biomedical ontologies.

Conclusions

Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

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科学网—[转载]Plant Genome Databases and Websites - 孙岳的博文

科学网—[转载]Plant Genome Databases and Websites - 孙岳的博文 | Plant Genomics | Scoop.it
General plant genomics resources

Phytozome: comparative genomics of plants.
PlantGDB: plant genome database
NCBI Plant Genomes Cent ... ,科学网
Biswapriya Biswavas Misra's insight:
General plant genomics resourcesPhytozome: comparative genomics of plants.PlantGDB: plant genome databaseNCBI Plant Genomes Central: Links to NCBI resources for plant genomics.Munich Information System for Protein Sequences.Arizona Genome InstituteClemson University Genomics InstituteChromatinDBCarbohydrate active enzymesCell Wall GenomicsPrimer3 primer design toolGene OntologyPlant OntologyMicroRNAsGRIN: Germplasm Resources Information NetworkThe Virtual Plant at NYU.Agricola, a Bibliographic database of citations to the agricultural literaturePhytome supports phylogenetic and functional analyses of predicted protein sequences across plants.OrthologID provide phylogenetic analysis of Arabidopsis, rice, Populus, and Chlamydomonas genesPlantTribes provides OrthoMCL clustering of plant proteins, developed as part of the Floral Genome Project.Gene expressionPLEXdb (Plant Expression Database) is a unified public resource for gene expression for plants and plant pathogens. http://www.plexdb.orgArrayExpress is a public repository for transcriptomics and related data at EBI. http://www.ebi.ac.uk/arrayexpress/http://signal.salk.eduMPSS (Massively Parallel Signature Sequencing) datasets for Arabidopsis, rice, and grape, at U Delaware: http://mpss.udel.eduBotany Array Resources (BAR). http://www.bar.utoronto.caGeneVestigator is a reference expression database and meta-analysis system for studying the expression and regulation of genes by summarizing information from hundreds of microarray experiments into easily interpretable results. https://www.genevestigator.ethz.ch/Gene Indices and EST resourcesThe Gene Index project (formerly, TIGR gene indices) http://compbio.dfci.harvard.edu/tgi/PlantTA: Plant Transcript Assemblies http://plantta.tigr.orgHarvEST: EST analysis resources for barley, Brachypodium, Citrus, Coffea, cowpea, soybean, rice, and wheat. http://harvest.ucr.edu/Arabidopsis resourcesTAIR (The Arabidopsis Information Resource) http://www.arabidopsis.org; http:// www.tair.org)Salk Institute Genome Analysis Laboratory. http://signal.salk.edu/AtGenExpress, a multinational effort to uncover the transcriptome of A. thaliana. http://www.arabidopsis.org/info/expression/ATGenExpress.jspBotany Array Resources (BAR). http://www.bar.utoronto.caArabidopsis small RNA project http://asrp.cgrb.oregonstate.edu/Arabidopsis MPSS data at U Delaware. http://mpss.udel.edu/at/Grasses and cereals: rice, maize, sorghum, wheat, barley, Brachypodium, et al.Gramene: A Resource for Comparative Grass Genomics http://www.gramene.orgGrain Genes 2.0: A Database for Triticeae and Avena. http://wheat.pw.usda.govSorghum genome sequence at Phytozome: www.phytozome.net/sorghumMaizeDB ( www.maizedb.org)Maize genome sequence at CSHL ( www.maizesequence.org)Oryza map; maize FPC map. Arizona Genome Institute. http://www.genome.arizona.edu/Maize and sorghum assembled gene islands (Methyl-filtration) http://magi.plantgenomics.iastate.edu/Brachpodium genome database www.brachybase.orgwww.modelcrop.orgBrachypodium genome database at Phytozome: www.phytozome.net/brachypodiumMarker Assisted Selection for wheat. http://maswheat.ucdavis.eduPanZea: Molecular and Functional Diversity of the Maize Genome www.panzea.orgMaize Oligonucleotide Array Project http://www.maizearray.org/Beijing Genome Institute Rice Information System (RISE): http://rise.genomics.org.cn/riceRice Annotation Project Database (RAP-DB) http://rapdb.dna.affrc.go.jp/TIGR rice genome annotation and resources. www.tigr.org/tdb/riceInternational Rice Research Institute http://www.irri.org/Rice MPSS data at U. Delaware http://mpss.udel.edu/rice/Legumes: Soybean, Medicago, Lotus, et al.Soybean genome sequence at Phytozome: www.phytozome.net/soybeanMedicago truncatula: a model for legume research ( www.medicago.org). Links to genome sequencing, functional genomics, comparative genomicsLegume Information System http://www.comparative-legumes.orgSoybase and the soybean breeders toolbox. http://soybase.agron.iastate.edu/Lotus japonicus genome project at Kazusa http://www.kazusa.or.jp/lotus/BeanGenes: a Phaseolus/Vigra database, including links to other useful sites. http://beangenes.cws.ndsu.nodak.edu/SoyMap: An integrated map of soybean for resolution and dissection of multiple genome duplication events. http://www.soymap.org/Soybean genome map at Southern Illinois University http://soybeangenome.siu.edu/Forest tree genomicsPopulus trichocarpa genome at Phytozome. http://www.phytozome.net/poplarDendrome is a collection of forest tree genome databases and other forest genetic information resources for the international forest genetics community. Dendrome is part of a larger collaborative effort to construct genome databases for major crop and forest species. http://dendrome.ucdavis.edu EucalyptusTreeGenes EST database: http://treegenes.ucdavis.eduPopulusDB expression database at Umea Sweden. http://www.populus.db.umu.se/Genomic tool development for the chestnut tree and other Fagaceae http://www.fagaceae.org/Other plant speciesInternational Grape Genome Project http://www.vitaceae.orgGrape genome sequence at Genoscope: http://www.genoscope.cns.fr/externe/English/Projets/Projet_ML/index.htmlGrape genome at Phytozome: www.phytozome.net/grapeGrape MPSS data at U Delaware http://mpss.udel.edu/grape/Genome Database of Rosaceae ( www.bioinfo.wsu.edu/gdr)Tomato genome projectSOL Genomics Network is a clade-oriented database containing genomic, genetic and taxonomic information for species in the families Solanaceae (e.g., tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to the Arabidopsis genome. www.sgn.cornell.eduCompositae genomics project http://compgenomics.ucdavis.edu/Mimulus, columbineThe Physcomitrella patens computational biology resources http://www.cosmoss.org/Physcomitrella patens genome at Phytozome: www.phytozome.net/physcomitrellaSelaginella moellendorfii genome sequence at Phytozome: www.phytozome.net/selaginellaCastor Bean Genome Database at TIGR. http://castorbean.tigr.org/Papaya Genome Project at University of Hawaii http://cgpbr.hawaii.edu/papaya/Brassica rapa genomeCotton genome database contains genomic, genetic and taxonomic information for cotton at USDA-ARS College Station TX. http://cottondb.org/Cotton Genome Database at the Plant Genome Mapping Laboratory, University of Georgia http://www.plantgenome.uga.edu/cotton/StartFrame.htmInternational Cotton Genome Initiative http://icgi.tamu.edu/Plant pathogen genomicsPseudomonas syringae comparative genomics www.pseudomonas-syringae.org
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PLOS ONE: Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species

PLOS ONE: Development of Transcriptomic Resources for Interrogating the Biosynthesis of Monoterpene Indole Alkaloids in Medicinal Plant Species | Plant Genomics | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
Biswapriya Biswavas Misra's insight:
Abstract

The natural diversity of plant metabolism has long been a source for human medicines. One group of plant-derived compounds, the monoterpene indole alkaloids (MIAs), includes well-documented therapeutic agents used in the treatment of cancer (vinblastine, vincristine, camptothecin), hypertension (reserpine, ajmalicine), malaria (quinine), and as analgesics (7-hydroxymitragynine). Our understanding of the biochemical pathways that synthesize these commercially relevant compounds is incomplete due in part to a lack of molecular, genetic, and genomic resources for the identification of the genes involved in these specialized metabolic pathways. To address these limitations, we generated large-scale transcriptome sequence and expression profiles for three species of Asterids that produce medicinally important MIAs: Camptotheca acuminata, Catharanthus roseus, and Rauvolfia serpentina. Using next generation sequencing technology, we sampled the transcriptomes of these species across a diverse set of developmental tissues, and in the case of C. roseus, in cultured cells and roots following elicitor treatment. Through an iterative assembly process, we generated robust transcriptome assemblies for all three species with a substantial number of the assembled transcripts being full or near-full length. The majority of transcripts had a related sequence in either UniRef100, the Arabidopsis thaliana predicted proteome, or the Pfam protein domain database; however, we also identified transcripts that lacked similarity with entries in either database and thereby lack a known function. Representation of known genes within the MIA biosynthetic pathway was robust. As a diverse set of tissues and treatments were surveyed, expression abundances of transcripts in the three species could be estimated to reveal transcripts associated with development and response to elicitor treatment. Together, these transcriptomes and expression abundance matrices provide a rich resource for understanding plant specialized metabolism, and promotes realization of innovative production systems for plant-derived pharmaceuticals.

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Transcriptome analysis of mature-fruit abscission control in olive

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Abstract

Mature-fruit abscission (MFA) is a genetically controlled process, through poorly characterized mechanisms in fleshy fruit that include extensive transcriptional changes. While global transcriptome analyses have used to immature-fruit abscission in fleshy-fruit, no global gene-expression changes specific to MFA have been described. Here we use pyrosequencing to characterize the transcriptomes of the olive abscission-zone (AZ) during cell separation in order to understand MFA control at a stage of AZ-activation. Analysis of gene expression from these AZs reveal that membrane microdomains involving sterols/sphingolipids and remorins together with signaling proteins are potentially involved in MFA. This is accompanied by gene activity related to sphingolipid turnover, suggesting potentially the involvement of long-chain base metabolism in regulating MFA. Activation of vesicle trafficking involving small-GTPases is probably required for cell-wall modifications during abscission. Analysis of transcription-factors indicates that most members of MYB and bZIP families are abundantly represented in fruit-AZ, and it is consistent with a model by which most of key transcription-factors during abscission may regulate downstream processes mostly related to abscisic acid. The data provide the first thorough analysis available for a comprehensive picture of the array of cellular responses controlled by gene-expression that lead to MFA in fleshy-fruit.

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Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease

Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease | Plant Genomics | Scoop.it
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Biswapriya Biswavas Misra's insight:
Abstract

Huanglongbing (HLB) or “citrus greening” is the most destructive citrus disease worldwide. In this work, we studied host responses of citrus to infection with Candidatus Liberibacter asiaticus (CaLas) using next-generation sequencing technologies. A deep mRNA profile was obtained from peel of healthy and HLB-affected fruit. It was followed by pathway and protein-protein network analysis and quantitative real time PCR analysis of highly regulated genes. We identified differentially regulated pathways and constructed networks that provide a deep insight into the metabolism of affected fruit. Data mining revealed that HLB enhanced transcription of genes involved in the light reactions of photosynthesis and in ATP synthesis. Activation of protein degradation and misfolding processes were observed at the transcriptomic level. Transcripts for heat shock proteins were down-regulated at all disease stages, resulting in further protein misfolding. HLB strongly affected pathways involved in source-sink communication, including sucrose and starch metabolism and hormone synthesis and signaling. Transcription of several genes involved in the synthesis and signal transduction of cytokinins and gibberellins was repressed while that of genes involved in ethylene pathways was induced. CaLas infection triggered a response via both the salicylic acid and jasmonic acid pathways and increased the transcript abundance of several members of the WRKY family of transcription factors. Findings focused on the fruit provide valuable insight to understanding the mechanisms of the HLB-induced fruit disorder and eventually developing methods based on small molecule applications to mitigate its devastating effects on fruit production.


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Transposable Elements Re-Wire and Fine-Tune the Transcriptome

Transposable Elements Re-Wire and Fine-Tune the Transcriptome | Plant Genomics | Scoop.it
PLOS Genetics is an open-access
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Abstract

What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs—particularly retrotransposons—contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.

 

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Transcriptome analysis of rice root heterosis by RNA-Seq

Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes.
Biswapriya Biswavas Misra's insight:
AbstractBackground

Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focused, root heterosis is also an indispensable component of heterosis in the entire plant and of major importance to plant breeding. Consequently, systematic investigations of root heterosis, particularly in reproductive-stage rice, are needed. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis studies.

Results

Using the Illumina HiSeq 2000 platform, the root transcriptomes of the super-hybrid rice variety Xieyou 9308 and its parents were analyzed at tillering and heading stages. Approximately 391 million high-quality paired-end reads (100-bp in size) were generated and aligned against the Nipponbare reference genome. We found that 38,872 of 42,081 (92.4%) annotated transcripts were represented by at least one sequence read. A total of 829 and 4186 transcripts that were differentially expressed between the hybrid and its parents (DGHP) were identified at tillering and heading stages, respectively. Out of the DGHP, 66.59% were down-regulated at the tillering stage and 64.41% were up-regulated at the heading stage. At the heading stage, the DGHP were significantly enriched in pathways related to processes such as carbohydrate metabolism and plant hormone signal transduction, with most of the key genes that are involved in the two pathways being up-regulated in the hybrid. Several significant DGHP that could be mapped to quantitative trait loci (QTLs) for yield and root traits are also involved in carbohydrate metabolism and plant hormone signal transduction pathways.

Conclusions

An extensive transcriptome dataset was obtained by RNA-Seq, giving a comprehensive overview of the root transcriptomes at tillering and heading stages in a heterotic rice cross and providing a useful resource for the rice research community. Using comparative transcriptome analysis, we detected DGHP and identified a group of potential candidate transcripts. The changes in the expression of the candidate transcripts may lay a foundation for future studies on molecular mechanisms underlying root heterosis.

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Transcriptome analysis of rice root heterosis

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.
Biswapriya Biswavas Misra's insight:

AbstractABSTRACT:

BACKGROUND: Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focused, root heterosis is also an indispensable component of heterosis in the entire plant and of major importance to plant breeding. Consequently, systematic investigations of root heterosis, particularly in reproductive-stage rice, are needed. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis studies.

RESULTS:

Using the Illumina HiSeq 2000 platform, the root transcriptomes of the super-hybrid rice variety Xieyou 9308 and its parents were analyzed at tillering and heading stages. Approximately 391 million high-quality paired-end reads (100-bp in size) were generated and aligned against the Nipponbare reference genome. We found that 38,872 of 42,081 (92.4%) annotated transcripts were represented by at least one sequence read. A total of 829 and 4186 transcripts that were differentially expressed between the hybrid and its parents (DGHP) were identified at tillering and heading stages, respectively. Out of the DGHP, 66.59% were down-regulated at the tillering stage and 64.41% were up-regulated at the heading stage. At the heading stage, the DGHP were significantly enriched in pathways related to processes such as carbohydrate metabolism and plant hormone signal transduction, with most of the key genes that are involved in the two pathways being up-regulated in the hybrid. Several significant DGHP that could be mapped to quantitative trait loci (QTLs) for yield and root traits are also involved in carbohydrate metabolism and plant hormone signal transduction pathways.

CONCLUSIONS:

An extensive transcriptome dataset was obtained by RNA-Seq, giving a comprehensive overview of the root transcriptomes at tillering and heading stages in a heterotic rice cross and providing a useful resource for the rice research community. Using comparative transcriptome analysis, we detected DGHP and identified a group of potential candidate transcripts. The changes in the expression of the candidate transcripts may lay a foundation for future studies on molecular mechanisms underlying root heterosis.

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Delayed flowering results in up to 50 percent increase in biofuel crop yield - News - BBSRC

Biswapriya Biswavas Misra's insight:
Abstract

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.

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De novo genetic variation revealed in somatic sectors of single Arabidopsis plants.

Read the latest article version by Marianne T Hopkins, Aaron M Khalid, Pei-Chun Chang, Karen C Vanderhoek, Dulcie Lai, Meghan D Doerr, Susan J Lolle, at F1000Research.
Biswapriya Biswavas Misra's insight:
Abstract

Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives. Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.

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Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq

Abscission is a mechanism by which plants shed entire organs in response to both developmental and environmental signals.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

Abscission is a mechanism by which plants shed entire organs in response to both developmental and environmental signals. Arabidopsis thaliana, in which only the floral organs abscise, has been used extensively to study the genetic, molecular and cellular processes controlling abscission. Abscission in Arabidopsis requires two genes that encode functionally redundant receptor-like protein kinases, HAESA (HAE) and HAESA-LIKE 2 (HSL2). Double hae hsl2 mutant plants fail to abscise their floral organs at any stage of floral development and maturation.

Results

Using RNA-Seq, we compare the transcriptomes of wild-type and hae hsl2 stage 15 flowers, using the floral receptacle which is enriched for abscission zone cells. 2034 genes were differentially expressed with a False Discovery Rate adjusted p < 0.05, of which 349 had two fold or greater change in expression. Differentially expressed genes were enriched for hydrolytic, cell wall modifying, and defense related genes. Testing several of the differentially expressed genes in INFLORESCENCE DEFICIENT IN ABSCISSION (ida) mutants shows that many of the same genes are co-regulated by IDA and HAE HSL2 and support the role of IDA in the HAE and HSL2 signaling pathway. Comparison to microarray data from stamen abscission zones show distinct patterns of expression of genes that are dependent on HAE HSL2 and reveal HAE HSL2- independent pathways.

Conclusion

HAE HSL2-dependent and HAE HSL2-independent changes in genes expression are required for abscission. HAE and HSL2 affect the expression of cell wall modifying and defense related genes necessary for abscission. The HAE HSL2-independent genes also appear to have roles in abscission and additionally are involved in processes such as hormonal signaling, senescence and callose deposition.

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Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa ...

The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants.

Results

In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data.

Conclusions

A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic traits in NR1 line. Further study of the unknown tags which were specifically expressed in Fer will help to explore desirable agronomic traits from wild species.

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De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity

Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation.
Biswapriya Biswavas Misra's insight:
Abstract (provisional)Background

Plants such as grapevine (Vitis spp.) display significant inter-cultivar genetic and phenotypic variation. The genetic components underlying phenotypic diversity in grapevine must be understood in order to disentangle genetic and environmental factors.

Results

We have shown that cDNA sequencing by RNA-seq is a robust approach for the characterization of varietal diversity between a local grapevine cultivar (Corvina) and the PN40024 reference genome. We detected 15,161 known genes including 9463 with novel splice isoforms, and identified 2321 potentially novel protein-coding genes in non-annotated or unassembled regions of the reference genome. We also discovered 180 apparent private genes in the Corvina genome which were missing from the reference genome.

Conclusions

The de novo assembly approach allowed a substantial amount of the Corvina transcriptome to be reconstructed, improving known gene annotations by robustly defining gene structures, annotating splice isoforms and detecting genes without annotations. The private genes we discovered are likely to be nonessential but could influence certain cultivar-specific characteristics. Therefore, the application of de novo transcriptome assembly should not be restricted to species lacking a reference genome because it can also improve existing reference genome annotations and identify novel, cultivar-specific genes.

 
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Transcriptomic Research around the Globe « Homologus

Transcriptomic Research around the Globe « Homologus | Plant Genomics | Scoop.it
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Transcriptomic Research around the Globe

From time to time, we update our trends section with latest data from NCBI GEO database. Few reports from the last two years are listed here.

Transcriptomic Research around the Globe

In our Trends Section

In our Trends Section – II

Today, we uploaded new data to the trends section again. USA is still the global leader in transcriptomics research, but, in terms of growth, China and Germany are doing much better than USA. Data also shows rapid growth of Illumina, but that is not a surprise in 2013.

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科学网—[转载]Plant Genome Databases and Websites - 孙岳的博文

科学网—[转载]Plant Genome Databases and Websites - 孙岳的博文 | Plant Genomics | Scoop.it
General plant genomics resources

Phytozome: comparative genomics of plants.
PlantGDB: plant genome database
NCBI Plant Genomes Cent ... ,科学网
Biswapriya Biswavas Misra's insight:
General plant genomics resources Phytozome: comparative genomics of plants. PlantGDB: plant genome database NCBI Plant Genomes Central: Links to NCBI resources for plant genomics. Munich Information System for Protein Sequences. Arizona Genome Institute Clemson University Genomics Institute ChromatinDB Carbohydrate active enzymes Cell Wall Genomics Primer3 primer design tool Gene Ontology Plant Ontology MicroRNAs GRIN: Germplasm Resources Information Network The Virtual Plant at NYU. Agricola, a Bibliographic database of citations to the agricultural literature Phytome supports phylogenetic and functional analyses of predicted protein sequences across plants. OrthologID provide phylogenetic analysis of Arabidopsis, rice, Populus, and Chlamydomonas genes PlantTribes provides OrthoMCL clustering of plant proteins, developed as part of the Floral Genome Project. Gene expression PLEXdb (Plant Expression Database) is a unified public resource for gene expression for plants and plant pathogens. http://www.plexdb.org ArrayExpress is a public repository for transcriptomics and related data at EBI. http://www.ebi.ac.uk/arrayexpress/ http://signal.salk.edu MPSS (Massively Parallel Signature Sequencing) datasets for Arabidopsis, rice, and grape, at U Delaware: http://mpss.udel.edu Botany Array Resources (BAR). http://www.bar.utoronto.ca GeneVestigator is a reference expression database and meta-analysis system for studying the expression and regulation of genes by summarizing information from hundreds of microarray experiments into easily interpretable results. https://www.genevestigator.ethz.ch/ Gene Indices and EST resources The Gene Index project (formerly, TIGR gene indices) http://compbio.dfci.harvard.edu/tgi/ PlantTA: Plant Transcript Assemblies http://plantta.tigr.org HarvEST: EST analysis resources for barley, Brachypodium, Citrus, Coffea, cowpea, soybean, rice, and wheat. http://harvest.ucr.edu/ Arabidopsis resources TAIR (The Arabidopsis Information Resource) http://www.arabidopsis.org; http:// www.tair.org) Salk Institute Genome Analysis Laboratory. http://signal.salk.edu/ AtGenExpress, a multinational effort to uncover the transcriptome of A. thaliana. http://www.arabidopsis.org/info/expression/ATGenExpress.jsp Botany Array Resources (BAR). http://www.bar.utoronto.ca Arabidopsis small RNA project http://asrp.cgrb.oregonstate.edu/ Arabidopsis MPSS data at U Delaware. http://mpss.udel.edu/at/ Grasses and cereals: rice, maize, sorghum, wheat, barley, Brachypodium, et al. Gramene: A Resource for Comparative Grass Genomics http://www.gramene.org Grain Genes 2.0: A Database for Triticeae and Avena. http://wheat.pw.usda.gov Sorghum genome sequence at Phytozome: www.phytozome.net/sorghum MaizeDB ( www.maizedb.org) Maize genome sequence at CSHL ( www.maizesequence.org) Oryza map; maize FPC map. Arizona Genome Institute. http://www.genome.arizona.edu/ Maize and sorghum assembled gene islands (Methyl-filtration) http://magi.plantgenomics.iastate.edu/ Brachpodium genome database www.brachybase.org www.modelcrop.org Brachypodium genome database at Phytozome: www.phytozome.net/brachypodium Marker Assisted Selection for wheat. http://maswheat.ucdavis.edu PanZea: Molecular and Functional Diversity of the Maize Genome www.panzea.org Maize Oligonucleotide Array Project http://www.maizearray.org/ Beijing Genome Institute Rice Information System (RISE): http://rise.genomics.org.cn/rice Rice Annotation Project Database (RAP-DB) http://rapdb.dna.affrc.go.jp/ TIGR rice genome annotation and resources. www.tigr.org/tdb/rice International Rice Research Institute http://www.irri.org/ Rice MPSS data at U. Delaware http://mpss.udel.edu/rice/ Legumes: Soybean, Medicago, Lotus, et al. Soybean genome sequence at Phytozome: www.phytozome.net/soybean Medicago truncatula: a model for legume research ( www.medicago.org). Links to genome sequencing, functional genomics, comparative genomics Legume Information System http://www.comparative-legumes.org Soybase and the soybean breeders toolbox. http://soybase.agron.iastate.edu/ Lotus japonicus genome project at Kazusa http://www.kazusa.or.jp/lotus/ BeanGenes: a Phaseolus/Vigra database, including links to other useful sites. http://beangenes.cws.ndsu.nodak.edu/ SoyMap: An integrated map of soybean for resolution and dissection of multiple genome duplication events. http://www.soymap.org/ Soybean genome map at Southern Illinois University http://soybeangenome.siu.edu/ Forest tree genomics Populus trichocarpa genome at Phytozome. http://www.phytozome.net/poplar Dendrome is a collection of forest tree genome databases and other forest genetic information resources for the international forest genetics community. Dendrome is part of a larger collaborative effort to construct genome databases for major crop and forest species. http://dendrome.ucdavis.edu Eucalyptus TreeGenes EST database: http://treegenes.ucdavis.edu PopulusDB expression database at Umea Sweden. http://www.populus.db.umu.se/ Genomic tool development for the chestnut tree and other Fagaceae http://www.fagaceae.org/ Other plant species International Grape Genome Project http://www.vitaceae.org Grape genome sequence at Genoscope: http://www.genoscope.cns.fr/externe/English/Projets/Projet_ML/index.html Grape genome at Phytozome: www.phytozome.net/grape Grape MPSS data at U Delaware http://mpss.udel.edu/grape/ Genome Database of Rosaceae ( www.bioinfo.wsu.edu/gdr) Tomato genome project SOL Genomics Network is a clade-oriented database containing genomic, genetic and taxonomic information for species in the families Solanaceae (e.g., tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to the Arabidopsis genome. www.sgn.cornell.edu Compositae genomics project http://compgenomics.ucdavis.edu/ Mimulus, columbine The Physcomitrella patens computational biology resources http://www.cosmoss.org/ Physcomitrella patens genome at Phytozome: www.phytozome.net/physcomitrella Selaginella moellendorfii genome sequence at Phytozome: www.phytozome.net/selaginella Castor Bean Genome Database at TIGR. http://castorbean.tigr.org/ Papaya Genome Project at University of Hawaii http://cgpbr.hawaii.edu/papaya/ Brassica rapa genome Cotton genome database contains genomic, genetic and taxonomic information for cotton at USDA-ARS College Station TX. http://cottondb.org/ Cotton Genome Database at the Plant Genome Mapping Laboratory, University of Georgia http://www.plantgenome.uga.edu/cotton/StartFrame.htm International Cotton Genome Initiative http://icgi.tamu.edu/ Plant pathogen genomics Pseudomonas syringae comparative genomics www.pseudomonas-syringae.org
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Plant J: QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations (2013)

Plant J: QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations (2013) | Plant Genomics | Scoop.it

The majority of agronomically important crop traits are quantitative, meaning that they are controlled by multiple genes each with a small effect (quantitative trait loci: QTL). QTL mapping and isolation is important for efficient crop breeding by marker-assisted selection (MAS) and for a better understanding of the molecular mechanisms underlying the traits. Since it requires the development and selection of DNA markers for linkage analysis, QTL analysis has been however time consuming and labor intensive. Here we report a rapid identification of plant QTL by whole genome resequencing of DNAs from two populations each composed of 20-50 individuals showing extreme opposite trait values for a given phenotype in a segregating progeny. We propose to name this approach QTL-seq as applied to plant species. We applied QTL-seq to rice recombinant inbred lines (RILs) and F2 populations and successfully identified QTL for important agronomic traits, such as partial resistance to the fungal rice blast disease and seedling vigor. Simulation study showed that QTL-seq is able to detect QTL over wide ranges of experimental variables, and the method can be generally applied in population genomics studies to rapidly identify genomic regions that underwent artificial or natural selective sweeps.


Via Kamoun Lab @ TSL
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Teresa M. Nash's comment, November 28, 2013 1:23 AM
Nice.