16 research outputs found
Recommended from our members
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
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid
<p>Abstract</p> <p>Background</p> <p>Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.</p> <p>Results</p> <p>RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed.</p> <p>Conclusions</p> <p>The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.</p
Recommended from our members
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
Recommended from our members
DharmawardhanaPalithaBotanyPlantPathologyGramene2013.pdf
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
Recommended from our members
DharmawardhanaPalithaBotanyPlantPathologyGramene2013_SupplementaryData.pdf
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