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PlantGDB specifications

Information


Unique identifier OMICS_04420
Name PlantGDB
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Volker Brendel

Publication for PlantGDB

PlantGDB citations

 (109)
library_books

The Sequenced Angiosperm Genomes and Genome Databases

2018
Front Plant Sci
PMCID: 5909171
PMID: 29706973
DOI: 10.3389/fpls.2018.00418

[…] genomes, which is less than one-eighth of total sequenced angiosperms.Many of these comprehensive genome databases are well-maintained and are frequently updated with release of new versions, such as PlantGDB V187, Phytozome V12, and Gramene V36. Phytozome updates roughly each year, and PGDD and CoGe update timely upon availability of new genome data. Another feature is that these databases are em […]

library_books

Genome Wide Characterization of Heat Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress

2018
Genes
PMCID: 5852552
PMID: 29360757
DOI: 10.3390/genes9020035

[…] ), Selaginella moellendorffii [], Amborella trichopoda (http://amborella.huck.psu.edu/), Spirodela polyrhiza [], Zostera marina (http://www.algaebase.org/search/), Brachypodium distachyon (http://www.plantgdb.org/BdGDB/), Oryza sativa (http://www.plantgdb.org/OsGDB/), Glycine max (http://www.plantgdb.org/GmGDB/), Brassica rapa (http://brassicadb.org/brad/), Arabidopsis thaliana (http://www.plantgd […]

library_books

Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice

2017
Front Plant Sci
PMCID: 5693882
PMID: 29181013
DOI: 10.3389/fpls.2017.01944

[…] (protein BLAST) in three different databases: NCBI (https://blast.ncbi.nlm.nih.gov/), phytozyme V.11 (https://phytozome.jgi.doe.gov/pz/portal.html), and plant genome database release 187 (http://www.plantgdb.org/), using Arabidopsis GATA1 protein sequence as the reference. Redundant sequences were omitted manually. Functional domains in the full-length protein sequence were identified using pfam, […]

library_books

Overexpression of the Maize ZmNLP6 and ZmNLP8 Can Complement the Arabidopsis Nitrate Regulatory Mutant nlp7 by Restoring Nitrate Signaling and Assimilation

2017
Front Plant Sci
PMCID: 5634353
PMID: 29051766
DOI: 10.3389/fpls.2017.01703

[…] e obtained trees was tested using a bootstrapping method with 1000 replicates. The images of the phylogenetic trees were drawn using MEGA7. The genomic and CDS of NLP members were downloaded from the plantGDB database. The gene structures of NLP genes were generated using the GSDS. The position of GAF-Like, RWP-RK and PB1 domain was indicated from the Pfam results. […]

library_books

Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories

2017
Front Plant Sci
PMCID: 5632664
PMID: 29046688
DOI: 10.3389/fpls.2017.01719

[…] ia a BLASTN search against the Arabidopsis genome on EnsemblPlants (http://plants.ensembl.org) and then putative proteins in Arabidopsis were searched via a tBLASTN (six frames) against the P. glauca PlantGDB Putative Unique Transcripts (PUTs) database on ConGenIE (http://congenie.org/). Each PUT underwent another BLASTN search against the Arabidopsis genome. Homologs were identified only if the s […]

library_books

Single Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

2017
Genome Biol Evol
PMCID: 5414570
PMID: 28460034
DOI: 10.1093/gbe/evx070

[…] elected a representative sequence from the clusters formed by the novel transcripts and the Newbler assemblies with 90% identity to remove redundant transcripts. For P. pinaster, we integrated 15,648 PlantGDB-assembled Unique Transcripts (PUTs, based on GenBank release 177) () and 210,513 unigenes from SustainPineDB (). For P. sylvestris, we integrated 73,609 PUTs (based on GenBank release 187) an […]

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PlantGDB institution(s)
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA

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