20 research outputs found
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A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress
Background: Functional annotations of large plant genome projects mostly provide information on gene function
and gene families based on the presence of protein domains and gene homology, but not necessarily in
association with gene expression or metabolic and regulatory networks. These additional annotations are necessary
to understand the physiology, development and adaptation of a plant and its interaction with the environment.
Results: RiceCyc is a metabolic pathway networks database for rice. It is a snapshot of the substrates, metabolites,
enzymes, reactions and pathways of primary and intermediary metabolism in rice. RiceCyc version 3.3 features 316
pathways and 6,643 peptide-coding genes mapped to 2,103 enzyme-catalyzed and 87 protein-mediated transport
reactions. The initial functional annotations of rice genes with InterPro, Gene Ontology, MetaCyc, and Enzyme
Commission (EC) numbers were enriched with annotations provided by KEGG and Gramene databases. The
pathway inferences and the network diagrams were first predicted based on MetaCyc reference networks and plant
pathways from the Plant Metabolic Network, using the Pathologic module of Pathway Tools. This was enriched by
manually adding metabolic pathways and gene functions specifically reported for rice. The RiceCyc database is
hierarchically browsable from pathway diagrams to the associated genes, metabolites and chemical structures.
Through the integrated tool OMICs Viewer, users can upload transcriptomic, proteomic and metabolomic data to
visualize expression patterns in a virtual cell. RiceCyc, along with additional species-specific pathway databases
hosted in the Gramene project, facilitates comparative pathway analysis.
Conclusions: Here we describe the RiceCyc network development and discuss its contribution to rice genome
annotations. As a case study to demonstrate the use of RiceCyc network as a discovery environment we carried out
an integrated bioinformatic analysis of rice metabolic genes that are differentially regulated under diurnal
photoperiod and biotic stress treatments. The analysis of publicly available rice transcriptome datasets led to the
hypothesis that the complete tryptophan biosynthesis and its dependent metabolic pathways including serotonin
biosynthesis are induced by taxonomically diverse pathogens while also being under diurnal regulation. The
RiceCyc database is available online for free access at http://www.gramene.org/pathway/.Keywords: Oryza sativa, Metabolic network, Diurnal, Serotonin biosynthesis, Auxin biosynthesis, Tryptophan biosynthesis, Rice, RiceCyc, Gene regulation, Biotic stres
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The genome of Eucalyptus grandis
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have
made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase
genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest
proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as
terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister
species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding
depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to
the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a
powerful tool to accelerate comparative biology, breeding and biotechnology
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Maize Metabolic Network Construction and Transcriptome Analysis
A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays L. subsp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary plant products, and other metabolites by annotating the genes identified in the maize reference genome sequenced from the B73 variety. MaizeCyc version 2.0.2 is a collection of 391 maize pathways involving 8889 enzyme mapped to 2110 reactions and 1468 metabolites. We used MaizeCyc to describe the development and function of maize organs including leaf, root, anther, embryo, and endosperm by exploring the recently published microarray-based maize gene expression atlas. We found that 1062 differentially expressed metabolic genes mapped to 524 unique enzymatic reactions associated with 310 pathways. The MaizeCyc pathway database was created by running a library of evidences collected from the maize genome annotation, gene-based phylogeny trees, and comparison to known genes and pathways from rice (Oryza sativa L.) and Arabidopsis thaliana (L.) Heynh. against the PathoLogic module of Pathway Tools. The network and the database that were also developed as a community resource are freely accessible online at http://maizecyc.maizegdb.org to facilitate analysis and promote studies on metabolic genes in maize.Keywords: Arabidopsis,
Bundle sheath,
Leaves,
C-4 photosynthesis,
Evolution,
Systems biology,
Plant,
Genome,
Biochemical pathway database,
Mode
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Gramene 2013: comparative plant genomics resources
Gramene (http://www.gramene.org) is a curated
online resource for comparative functional
genomics in crops and model plant species, currently
hosting 27 fully and 10 partially sequenced
reference genomes in its build number 38. Its
strength derives from the application of a phylogenetic
framework for genome comparison and the
use of ontologies to integrate structural and functional
annotation data. Whole-genome alignments
complemented by phylogenetic gene family trees
help infer syntenic and orthologous relationships.
Genetic variation data, sequences and genome
mappings available for 10 species, including
Arabidopsis, rice and maize, help infer putative
variant effects on genes and transcripts. The
pathways section also hosts 10 species-specific
metabolic pathways databases developed in-house
or by our collaborators using Pathway Tools
software, which facilitates searches for pathway,
reaction and metabolite annotations, and allows
analyses of user-defined expression datasets.
Recently, we released a Plant Reactome portal
featuring 133 curated rice pathways. This portal
will be expanded for Arabidopsis, maize and other
plant species. We continue to provide genetic and
QTL maps and marker datasets developed by crop researchers. The project provides a unique community
platform to support scientific research in plant
genomics including studies in evolution, genetics,
plant breeding, molecular biology, biochemistry
and systems biology
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Gramene 2016: comparative plant genomics and pathway resources
Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials
No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss)
When salmonid fish that have been raised in hatcheries spawn in the wild, they often produce fewer surviving adult offspring than wild fish. Recent data from steelhead (Oncorhynchus mykiss) in the Hood River (Oregon, USA) show that even one or two generations of hatchery culture can result in dramatic declines in fitness. Although intense domestication selection could cause such declines, it is worth considering alternative explanations. One possibility is heritable epigenetic changes induced by the hatchery environment. Here, we show, using methylation-sensitive amplified fragment length polymorphism, that hatchery and wild adult steelhead from the Hood River do not appear to differ substantially in overall levels of genomic methylation. Thus, although altered methylation of specific DNA sites or other epigenetic processes could still be important, the hatchery environment does not appear to cause a global hypo- or hypermethylation of the genome or create a large number of sites that are differentially methylated
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ViningKellyForestryGenomeEucalyptusGrandis.pdf
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have
made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase
genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest
proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as
terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister
species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding
depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to
the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a
powerful tool to accelerate comparative biology, breeding and biotechnology
Recommended from our members
ViningKellyForestryGenomeEucalyptusGrandis_SupplementaryInformation.zip
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have
made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase
genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest
proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as
terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister
species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding
depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to
the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a
powerful tool to accelerate comparative biology, breeding and biotechnology