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Protocols

PopGenIE specifications

Information


Unique identifier OMICS_28072
Name PopGenIE
Alternative name Populus Genome Integrative Explorer
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Stefan Jansson

Publication for Populus Genome Integrative Explorer

PopGenIE citations

 (21)
library_books

The Sequenced Angiosperm Genomes and Genome Databases

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

[…] se containing genome data, genomic tools, and breeders' tools.Other clade-oriented genome databases host <10 genomes (Figure ), such as the Rosaceae crop oriented GDR (Jung et al., ), poplar oriented PopGenIE (Sjödin et al., ), cool season food legume oriented CSFL (Main et al., ). These clade-oriented genome databases gather multiple species, often with economic importance from the same clade, an […]

library_books

Ethylene Related Gene Expression Networks in Wood Formation

2018
Front Plant Sci
PMCID: 5861219
PMID: 29593753
DOI: 10.3389/fpls.2018.00272

[…] rs and quality trimming of sequences was performed as described in Felten et al. (). Read pairs that passed the quality assessment were mapped to the latest P. tremula genome sequence retrieved from “PopGenIE” (www.popgenie.org). We chose the P. tremula genome since its genetic background is most similar to hybrid aspen (P. tremula × tremuloides; Hamzeh and Dayanandan, ), which was the species use […]

library_books

Slow evolution of sex‐biased genes in the reproductive tissue of the dioecious plant Salix viminalis

2018
Mol Ecol
PMCID: 5901004
PMID: 29274186
DOI: 10.1111/mec.14466

[…] Additional to S. viminalis, we obtained coding sequences for P. trichocarpa from Ensembl Plants 32 (Flicek et al., ), Populus tremula and Populus tremuloides from PopGenIE (Sundell et al., ) and Salix suchowensis (http://115.29.234.170/willow/ (Dai et al., )). The longest transcript for each gene was identified in all species, and a reciprocal blastn with an e‐ […]

library_books

Characterization of the basic helix–loop–helix gene family and its tissue differential expression in response to salt stress in poplar

2018
PeerJ
PMCID: 5857177
PMID: 29576971
DOI: 10.7717/peerj.4502

[…] Subcellular localization of bHLH proteins was predicted by WoLF PSORT (). Gene coordinate was identified by PopGenIE v3.0 database (). […]

call_split

Control of chrysanthemum flowering through integration with an aging pathway

2017
Nat Commun
PMCID: 5635119
PMID: 29018260
DOI: 10.1038/s41467-017-00812-0
call_split See protocol

[…] .org) and OsNF-YB8 (AB095440); BnNF-YB8 (AHI94926) and MtNF-YB8 (AFK49658) sequences were obtained from NCBI (http://www.ncbi.nlm.nih.gov/); PtNF-YB8 (Potri.008G044800.1) sequences were obtained from PopGenIE (http://popgenie.org/). A. thaliana NF-YB family sequences were obtained from the TAIR database: AtNF-YB1 (AT2G38880), AtNF-YB2 (AT5G47640), AtNF-YB3 (AT4G14540), AtNF-YB4 (AT1G09030), AtNF-Y […]

library_books

Population genomics of the eastern cottonwood (Populus deltoides)

2017
Ecol Evol
PMCID: 5696417
PMID: 29187979
DOI: 10.1002/ece3.3466

[…] erent approaches (Tajima's D and X T X outliers, and environmental associations identified with LFMM and BAYENV2) were tested for gene function enrichment using Fisher's exact test implemented in the Populus Genome Integrative Explorer (PopGenIE; http://popgenie.org/; Sjödin, Street, Sandberg, Gustafsson, & Jansson, ). This database allows testing for enrichment for the gene ontology (GO) categori […]

Citations

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PopGenIE institution(s)
Umea Plant Science Centre, Department of Plant Physiology, University of Umea, Umea, Sweden; CBRN Security and Defence, Swedish Defence Research Agency, Umea, Sweden
PopGenIE funding source(s)
Supported by grants from the Swedish Research Council, the Swedish Research Council for the Environment, Agricultural Sciences and Spatial Planning, the Swedish Foundation for Strategic Research, The Knut and Alice Wallenberg Foundation and the Kempe Foundation.

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