Chia () is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.
View Article and Find Full Text PDFLarge-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization.
View Article and Find Full Text PDFPlant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase.
View Article and Find Full Text PDFThe availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pan-genomes of several crops. The pan-genomes of crops constructed from various cultivars, accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives.
View Article and Find Full Text PDFModeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence.
View Article and Find Full Text PDFThe Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms.
View Article and Find Full Text PDFEnsembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.
View Article and Find Full Text PDFLectins are ubiquitous proteins that reversibly bind to specific carbohydrates and, thus, serve as readers of the sugar code. In photosynthetic organisms, lectin family proteins play important roles in capturing and releasing photosynthates via an endogenous lectin cycle. Often, lectin proteins consist of one or more lectin domains in combination with other types of domains.
View Article and Find Full Text PDFChia ( L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and development and genetic improvement.
View Article and Find Full Text PDFThe S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the -locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants.
View Article and Find Full Text PDFGramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide.
View Article and Find Full Text PDFPlant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project.
View Article and Find Full Text PDFBiocuration plays a crucial role in building databases and complex systems-level platforms required for processing, annotating and analyzing 'Big Data' in biology. However, biocuration efforts cannot keep pace with a dramatic increase in the production of omics data; this presents one of the bottlenecks in genomics. In two pathway curation jamborees, Plant Reactome curators tested strategies for introducing researchers to pathway curation tools, harnessing biologists' expertise in curating plant pathways and developing a network of community biocurators.
View Article and Find Full Text PDFThe future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research.
View Article and Find Full Text PDFGramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species.
View Article and Find Full Text PDFGramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering.
View Article and Find Full Text PDFMethods Mol Biol
January 2018
The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g.
View Article and Find Full Text PDFPlant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project.
View Article and Find Full Text PDFFragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4.
View Article and Find Full Text PDFGramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species.
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