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Coffee Genome Hub specifications

Information


Unique identifier OMICS_06474
Name Coffee Genome Hub
Restrictions to use None
Maintained Yes

Publication for Coffee Genome Hub

Coffee Genome Hub citations

 (4)
call_split

Identification and Analysis of Jasmonate Pathway Genes in Coffea canephora (Robusta Coffee) by In Silico Approach

2017
PMCID: 5538154
PMID: 28808380
DOI: 10.4103/pm.pm_518_16
call_split See protocol

[…] f different genes involved in the JA synthesis was taken from the model plant A. thaliana using NCBI database. Those sequences were used for Basic Local Alignment Search Tool (BLAST) search[] and the Coffee Genome Hub database to identify the respective gene sequences in C. canephora. Among the matches in C. canephora, top match for each gene was taken and used for BLAST search against NCBI databa […]

library_books

A genome wide analysis of the RNA guided silencing pathway in coffee reveals insights into its regulatory mechanisms

2017
PLoS One
PMCID: 5407642
PMID: 28448529
DOI: 10.1371/journal.pone.0176333

[…] tomato (Solanum lycopersicum) []; eight in rice (O. sativa) []; and six in common bean (P. vulgaris) [].The annotated protein-coding sequences identified from the BLASTP of the DCL-like search in the Coffee Genome Hub were retrieved, and conserved domain analysis revealed that nine of these sequences contained DCL-like conserved domains (). Two of the sequences (Cc02_14900 and Cc02_14910) that are […]

call_split

Evolutionary Analyses of GRAS Transcription Factors in Angiosperms

2017
Front Plant Sci
PMCID: 5332381
PMID: 28303145
DOI: 10.3389/fpls.2017.00273
call_split See protocol

[…] in syntenic blocks was retrieved using SynMap program (http://genomevolution.org/CoGe/SynMap.pl) obtained using a default parameter (Lyons et al., ) except for C. canephora which was studied with the Coffee Genome Hub (http://coffee-genome.org/syntenic_dotplot) (Dereeper et al., ). […]

library_books

Shift in precipitation regime promotes interspecific hybridization of introduced Coffea species

2016
Ecol Evol
PMCID: 4829533
PMID: 27096083
DOI: 10.1002/ece3.2055

[…] lymorphism information content (PIC) according to Poncet et al. (, ). PCR conditions and all information on the markers are given in MoccaDB (http://moccadb.mpl.ird.fr; Plechakova et al. ) and in the coffee genome hub (Dereeper et al. ).Two chloroplastic microsatellite (cpSSRs) loci, with species‐specific alleles, were designed based on sequences published by Tesfaye et al. (). The first cpSSR, MS […]

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Coffee Genome Hub institution(s)
UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), Montpellier, France; UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, Montpellier, France; Bioversity International, Parc Scientifique Agropolis II, Montpellier, France; UMR Diversité Adaptation et DEveloppement des plantes (DIADE), Institut de Recherche pour le Développement (IRD), Montpellier, France

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