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Protocols

CGD specifications

Information


Unique identifier OMICS_32154
Name CGD
Alternative name Citrus Genome Database
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Additional information


https://www.citrusgenomedb.org/userManual

CGD citations

 (11)
library_books

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

2017
PMCID: 5727400
DOI: 10.1093/database/bax092

[…] e i5k Workspace (https://i5k.nal.usda.gov/) (), the Cool Season Food Legume Database (CSFL, https://www.coolseasonfoodlegume.org) (), the Legume Information System (http://legumeinfo.org/) () and the Citrus Genome Database (CGD, http://www.citrusgenomedb.org) (). For a more extensive list of databases currently using Tripal see https://tripal.info.Drupal, an open source, popular and well-supported […]

library_books

Genome resequencing and transcriptome profiling reveal structural diversity and expression patterns of constitutive disease resistance genes in Huanglongbing tolerant Poncirus trifoliata and its hybrids

2017
PMCID: 5686287
PMID: 29152310
DOI: 10.1038/hortres.2017.64

[…] Poncirus ESTs were downloaded from the citrus genome database (https://www.citrusgenomedb.org/species/trifoliata/unigene1.0). The Arabidopsis CDR1 gene sequence was used in BLASTP searches against the EST database to identify CDR genes-rel […]

library_books

Development of single copy nuclear intron markers for species level phylogenetics: Case study with Paullinieae (Sapindaceae)1

2017
Appl Plant Sci
PMCID: 5628028
PMID: 28989824
DOI: 10.3732/apps.1700051

[…] The ‘Citrus sinensis CDS’ (46,147 sequences; C. sinensis genome version 1.0) and genome annotation files were downloaded from the Citrus Genome Database (www.citrusgenomedb.org [accessed 22 August 2015]; ). Sequences in this CDS file are mature mRNA strands void of introns and untranslated regions. Of these 46,147 mature mRNAs, […]

call_split

Solar thermotherapy reduces the titer of Candidatus Liberibacter asiaticus and enhances canopy growth by altering gene expression profiles in HLB affected citrus plants

2017
PMCID: 5615044
PMID: 28955443
DOI: 10.1038/hortres.2017.54
call_split See protocol

[…] e read numbers for each gene were counted using STAR with a maximum intron 5000 bp (−alignIntronMax 5000). The Citrus clementina reference genome and corresponding annotation were downloaded from the Citrus Genome Database (http://www.citrusgenomedb.org/). Differentially expressed (DE) genes between each group were identified using the DESeq2 Bioconductor package. Raw counts of each gene were norm […]

library_books

Variability in CitXET expression and XET activity in Citrus cultivar Huangguogan seedlings with differed degrees of etiolation

2017
PLoS One
PMCID: 5472283
PMID: 28617857
DOI: 10.1371/journal.pone.0178973

[…] iciosa (L46792.1), Vitis vinifera (AY043238.1), Solanum lycopersicum (D16456.1), Fragaria chiloensis (GQ280283.1), Pyrus pyrifolia (EU432411.1), and Malus domestica (AY144593.1). We also searched the Citrus Genome Database (http://citrus.hzau.edu.cn) to identify the homologous citrus XET gene (CitXET). The Primer 3.0 online tool (http://bioinfo.ut.ee/primer3-0.4.0/) was used to design CitXET-speci […]

library_books

Alternative oxidase (AOX) constitutes a small family of proteins in Citrus clementina and Citrus sinensis L. Osb

2017
PLoS One
PMCID: 5411082
PMID: 28459876
DOI: 10.1371/journal.pone.0176878

[…] The identification and structural analysis of the AOX genes (introns/exons) were performed using the Citrus Genome Database (https://www.citrusgenomedb.org/). Open reading frame (ORF) analysis was performed using the ORFinder software (http://www.ncbi.nlm.nih.gov/orffinder/). The prediction of the th […]

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