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Protocols

PlantTribes specifications

Information


Unique identifier OMICS_03255
Name PlantTribes
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Carica papaya
    • Medicago truncatula
    • Oryza sativa
    • Populus trichocarpa

Publication for PlantTribes

PlantTribes citations

 (10)
library_books

Transcriptome profiling of tobacco (Nicotiana tabacum) pollen and pollen tubes

2017
BMC Genomics
PMCID: 5545845
PMID: 28784084
DOI: 10.1186/s12864-017-3972-3

[…] nst a list of 357 UCO protein sequences from Arabidopsis (sequences available at: http://compgenomics.ucdavis.edu/compositae_reference.php). Finally, the translated unigenes were compared against the PlantTribes database [, ]. In this analysis, 983 shared single copy tribes from Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa were compared with the translated unigenes us […]

library_books

Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty

2014
Mol Biol Evol
PMCID: 4327159
PMID: 25534030
DOI: 10.1093/molbev/msu343

[…] ted if it returned a hit with an E value smaller than 1e-10 and at least 30 amino acids long. Results from this analysis shown in indicate that gene coverage ranged from at least 90% in Phelipanche (PlantTribes single copy analysis) to 100% (UCO analysis) in Triphysaria combined assemblies. These results suggested that our assemblies have excellent gene coverage and are very likely to capture the […]

library_books

Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas]

2014
PLoS One
PMCID: 3946583
PMID: 24608103
DOI: 10.1371/journal.pone.0090895

[…] ete sequences and some experiment validations will be helpful to identified unclassified TEs. It is noteworthy that few of the 1,405 TEs were collected with full length in plant repeat databases like PlantTribes or Repbase , . All the TEs identified in sweet potato are summarized in .The 1,405 TEs were submitted to GenBank for similarity alignment using BLASTn program and the result showed that th […]

library_books

Functional genomics of a generalist parasitic plant: Laser microdissection of host parasite interface reveals host specific patterns of parasite gene expression

2013
BMC Plant Biol
PMCID: 3636017
PMID: 23302495
DOI: 10.1186/1471-2229-13-9

[…] EARCH [] to remove similar (sub)sequences (to create non-redundant de novo assemblies). The post-processed unigenes for each build were then queried (BLASTx, 1e-5) against the 10 genomic proteomes in PlantTribes 2.0 [,] and assigned to PlantTribes 2.0 Orthogroups based on the cluster containing the best BLAST hit. Expression levels for each unigene was determined by mapping reads back to de novo a […]

library_books

The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm specific lineage

2012
BMC Genomics
PMCID: 3394424
PMID: 22759610
DOI: 10.1186/1471-2164-13-S3-S1

[…] The nucleotide sequences and corresponding amino acid sequences for the representative taxa were collected from various public databases, including GenBank, PlantGDB and PlantTribes [-]. The inferred transcript sequences for C. atlantica, C. harringtonia, P. abies, P. lambertiani, P. macrophyllus, P. palustris, P. sylvestris, S. verticillata, S. sempervirens, T. bacca […]

library_books

Exploring the Switchgrass Transcriptome Using Second Generation Sequencing Technology

2012
PLoS One
PMCID: 3315583
PMID: 22479570
DOI: 10.1371/journal.pone.0034225

[…] switchgrass ESTs that showed a positive hit to the UCO sequences with amino acid alignments of at least 30 residues. We assessed the transcriptome coverage by comparing the switchgrass ESTs with the PlantTribes database , . In this analysis 959 shared single copy tribes from Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa were compared with the switchgrass EST reads usi […]

Citations

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PlantTribes institution(s)
Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; Department of Plant Biology, University of Georgia, Athens, GA, USA; Nees Institute for the Biodiversity of Plants, University of Bonn, Bonn, Germany; Molecular Evolution and Bioinformatics Group, NERC Centre for Ecology and Hydrology, Mansfield Road, Oxford, UK; Department of Statistics and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
PlantTribes funding source(s)
Supported by National Science Foundation (DEB 0115684, DEB0638595 and DBI-0501890) and a scholarship from the Deutsche Telekom Stiftung.

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