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Gramene 2013: comparative plant genomics resources
2013
Nucleic Acids Research
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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 ...
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 ...
ACKNOWLEDGEMENTS The authors are evermore grateful to Gramene's users for their valuable suggestions and feedback in improving the overall quality of Gramene as a community resource. ...
doi:10.1093/nar/gkt1110
pmid:24217918
pmcid:PMC3964986
fatcat:lcgbm3znjnaptk4vprqeoowt34
Gramene 2016: comparative plant genomics and pathway resources
2015
Nucleic Acids Research
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Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. ...
Gramene's archive website (http://archive.gramene.org) continues to pro-vide previously reported resources on comparative maps, markers and QTL. ...
as a community resource. ...
doi:10.1093/nar/gkv1179
pmid:26553803
pmcid:PMC4702844
fatcat:q6fdmpjqxnarxerc6qokt6i6ui
Gramene QTL database: development, content and applications
2009
Database: The Journal of Biological Databases and Curation
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Introduction Gramene is a comparative genome database for plants that integrates information about genetic and physical maps, sequences, markers, germplasm resources, genes, proteins, pathways and phenotypes ...
Recently, Gramene has expanded its coverage of the plant kingdom to include several key dicotyledonous species, making it an even more powerful comparative genomic resource for plants and broadening its ...
doi:10.1093/database/bap005
pmid:20157478
pmcid:PMC2790302
fatcat:thesfvm7mbdefmpgm4qjtg7jva
GrameneMart: the BioMart data portal for the Gramene project
2012
Database: The Journal of Biological Databases and Curation
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Acknowledgements We would like to thank our users for their feedback and support as well as our collaborators and contributors who have supplied Gramene with data. ...
We would also like to thank the BioMart team at the Ontario Institute for Cancer Research (OICR) for developing and supporting the BioMart software, and also to the Ensembl and Ensembl Genomes teams at ...
Project description The Gramene project (http://www.gramene.org) was launched in March 2001 as a curated, open-source, Webaccessible data resource for comparative genome analysis (1) . ...
doi:10.1093/database/bar056
pmid:22374386
pmcid:PMC3289142
fatcat:as6r2h3em5djvgmvmtuns6k5nu
Ensembl Genomes 2013: scaling up access to genome-wide data
2013
Nucleic Acids Research
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In the context of Ensembl Plants, for example, we work closely with the Gramene database (http://www.gramene.org) (8) and a number of leading European plant genomics and informatics centers through the ...
pombe; and PhytoPath (http:// www.phytopathdb.org), a resource for plant pathogens, with a focus on fungi and oomycetes. ...
The barley genome represented in Ensembl Plants. ...
doi:10.1093/nar/gkt979
pmid:24163254
pmcid:PMC3965094
fatcat:bzydx6qowvdunnkte5sioqgk5y
FROM PLANT GENOMES TO PROTEIN FAMILIES: COMPUTATIONAL TOOLS
2013
Computational and Structural Biotechnology Journal
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The access to the primary DNA sequence has become a fundamental resource in biology. ...
According to the Genomes On-Line Database (GOLD), more than 20 plant genomes have been already completed and there are more than 200 ongoing plant genomic projects. ...
Figure 1 . 1 State-of-art of plant genome sequencing projects with available sequences.
© 2013 Martinez. ...
doi:10.5936/csbj.201307001
pmid:24688740
pmcid:PMC3962197
fatcat:pz33c37r2jdrpdzccpqo4txm5i
Maize Metabolic Network Construction and Transcriptome Analysis
2013
The Plant Genome
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metabolites by annotating the genes identified in the maize reference genome sequenced from the B73 variety. ...
To create such a framework for Zea mays ssp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary plant products, and other ...
This work was supported by the NSF Plant Genome Research Resource grant award IOS:0703908 (Gramene: A Platform for Comparative Plant Genomics), and the USDA-ARS and National Corn Growers Association (The ...
doi:10.3835/plantgenome2012.09.0025
fatcat:jwvh2brlyzcvbd6uymhqrm27iu
Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)
2013
Applications in Plant Sciences
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Beauv. ( Wolny et al., 2011 ) , which has a sequenced genome of 272 Mb and fi ve chromosomes. ...
(slender falsebrome; Poaceae), with an estimated genome size of 470 Mb and 17 chromosomes ( Foote et al., 2004 ) , is a perennial bunchgrass native to Europe, Asia, and North Africa and is closely related ...
Thanks to Sharon Wei and Doreen Ware from Gramene database, and Henry Priest and Todd Mockler from BrachyBase for help with the integration of data sets in the respective databases. ...
doi:10.3732/apps.1200011
pmid:25202520
pmcid:PMC4105277
fatcat:iiirvqvddngpdelpohaxfxpvnm
Unlocking Triticeae genomics to sustainably feed the future
2013
Plant and Cell Physiology
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Comparative genomics and integration of genomic resources from Triticeae plants and the model grass Brachypodium distachyon are aiding the discovery of new genes and functional analyses of genes in Triticeae ...
The availability of these genomic resources for Triticeae plants and innovative analytical applications using next-generation sequencing technologies are helping to revitalize our approaches in genetic ...
Acknowledgments The authors thank Tetsuya Sakurai, Takuhiro Yoshida of the RIKEN Center for Sustainable Resource Science for their data generation of cDNA mapping among Pooideae plants. ...
doi:10.1093/pcp/pct163
pmid:24204022
pmcid:PMC3856857
fatcat:uuepryp45rhk3etegnzb3sedka
Metabolomics in Plants and Humans: Applications in the Prevention and Diagnosis of Diseases
2013
BioMed Research International
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In the recent years, there has been an increase in the number of metabolomic approaches used, in parallel with proteomic and functional genomic studies. ...
In this review, we emphasize the use and application of metabolomics in human diseases and plant research to improve human health. ...
Thus, metabolomic studies compared with genomics or proteomics reflect changes in phenotype and function of a particular tissue, or organism. ...
doi:10.1155/2013/792527
pmid:23986911
pmcid:PMC3748395
fatcat:wygdv2jcgzbgfjh2566uz7vvqe
Transcriptome Analyses in Legumes: A Resource for Functional Genomics
2013
The Plant Genome
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The recent availability of genome sequence of several legume plants has helped boosting genomics research. ...
Legumes represent an important family of flowering plants in terms of providing human nutrition and capacity to fix atmospheric nitrogen for agricultural sustainability. ...
Acknowledgements The work on chickpea genomics is funded by the Department of Biotechnology ...
doi:10.3835/plantgenome2013.04.0011
fatcat:rzcyoc5vbnd73naorwjnj64bta
Rice DB: anOryzaInformation Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis
2013
The Plant Journal
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designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant ...
We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. ...
© 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd., The Plant Journal, (2013), 76, 1057-1073 ...
doi:10.1111/tpj.12357
pmid:24147765
pmcid:PMC4253041
fatcat:wbl27z3z2negtkaibkjnjqiapi
From Bench to Barn: Plant Model Research and its Applications in Agriculture
2013
Advancements in Genetic Engineering
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/mapping tool
http://signal.salk.edu/cgi-bin/RiceGE
Obtain full-length cDNA clones
(http://cdna01.dna.affrc.go.jp/cDNA/)
Monocots
GRAMENE
for comparative genome analysis to study cross-species ...
The Populus trichocarpa genome is comparatively small (550 Mb); it was the first tree genome to be fully sequenced [5] (Table 1) . ...
doi:10.4172/2169-0111.1000110
fatcat:jokcndq7lnci3aq5646ay7goci
Current status of genomic resources on wild relatives of rice
2020
Breeding Science
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But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. ...
, designing of molecular markers, comparative analysis and evolutionary biology studies. ...
Gramene Database Gramene is an integrated database developed for the comparative functional genomics in various plant species. ...
doi:10.1270/jsbbs.19064
pmid:32523396
pmcid:PMC7272243
fatcat:tn7j2ighmvaupmdiszssa5pzgy
PlantGSEA: a gene set enrichment analysis toolkit for plant community
2013
Nucleic Acids Research
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By adopting annotations from diverse resources, we found that the proportion of annotated genes increased in a promising way comparing with of single GO annotation (Supplementary Table S1 ). ...
from various resources. ...
doi:10.1093/nar/gkt281
pmid:23632162
pmcid:PMC3692080
fatcat:lchx36d4qrdrvhbjkwnphijata
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