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Gramene 2013: comparative plant genomics resources

Marcela K. Monaco, Joshua Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson (+14 others)
2013 Nucleic Acids Research  
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

Marcela K. Tello-Ruiz, Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule (+20 others)
2015 Nucleic Acids Research  
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

Junjian Ni, Anuradha Pujar, Ken Youens-Clark, Immanuel Yap, Pankaj Jaiswal, Isaak Tecle, Chih-Wei Tung, Liya Ren, William Spooner, Xuehong Wei, Shuly Avraham, Doreen Ware (+2 others)
2009 Database: The Journal of Biological Databases and Curation  
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

W. Spooner, K. Youens-Clark, D. Staines, D. Ware
2012 Database: The Journal of Biological Databases and Curation  
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

Paul Julian Kersey, James E. Allen, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall (+21 others)
2013 Nucleic Acids Research  
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

Manuel Martinez
2013 Computational and Structural Biotechnology Journal  
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

Marcela K. Monaco, Taner Z. Sen, Palitha D. Dharmawardhana, Liya Ren, Mary Schaeffer, Sushma Naithani, Vindhya Amarasinghe, Jim Thomason, Lisa Harper, Jack Gardiner, Ethalinda K.S. Cannon, Carolyn J. Lawrence (+2 others)
2013 The Plant Genome  
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)

Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, Pankaj Jaiswal
2013 Applications in Plant Sciences  
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

K. Mochida, K. Shinozaki
2013 Plant and Cell Physiology  
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

Diego F. Gomez-Casati, Maria I. Zanor, María V. Busi
2013 BioMed Research International  
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

Rohini Garg, Mukesh Jain*
2013 The Plant Genome  
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

Reena Narsai, James Devenish, Ian Castleden, Kabir Narsai, Lin Xu, Huixia Shou, James Whelan
2013 The Plant Journal  
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

Andrea Pitzschke
2013 Advancements in Genetic Engineering  
/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

Richa Kamboj, Balwant Singh, Tapan Kumar Mondal, Deepak Singh Bisht
2020 Breeding Science  
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

Xin Yi, Zhou Du, Zhen Su
2013 Nucleic Acids Research  
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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