How to contribute to CGD
Please contact us to arrange transfer of data to the Citrus Genome Database from accepted peer reviewed work. Manuscripts accepted in scientific journals are highly encouraged to submit data to the CGD prior to publication. After dataset submission, the CGD will provide an accession number and the data will be initially available for download on the publication datasets page. The data will then be integrated with existing CGD data, with full credit given to the submitting authors. As an active member of the AgBioData Consortium, we embrace the Findable, Accessible, Interoperable, and Reusable (FAIR) principles to facilitate and maximize the accessibility and reuse of large-scale data in agricultural research.
Citrus Genome Database partnership with Tree Genetics and Genomes (TGG)
Since July 18, 2011, all manuscripts containing genomics, genetics or breeding data for Citrus tree species, which have been accepted for publication in Tree Genetics and Genomes, will be required to submit data to the Citrus Genome Database prior to manuscript publication. On submission of the data, an accession number will be provided to the authors for inclusion in their publication. The data will remain private in the Citrus Genome Database until the date of publication release. In the longer term we will work to fully integrate each data set with existing CGD data, with full credit given to the submitting authors. Please contact us (selecting TGG DataSubmission in the category dropdown) to arrange transfer of data from manuscripts accepted for publication in TGG. We have easy to use templates for data transfer and will work closely with authors to ensure this process is expediated quickly and easily.
Data types and submission requirements
- Genome assembly and annotation data
- At minimum we need the FASTA of the assembly and the GFF3 of the annotated features. Ideally the data is also deposited into a standard repository (e.g. NCBI) and the accession number(s) are provided.
- Gene annotation data
- If you have functionally characterized a gene from a genome sequence, please provide the information via this template.
- Genome wide expression (RNA-seq) data
- We require the NCBI BioProject and associated BioSample accession numbers as well as expression values (example file)
- High-throughput sequencing data
- We do not accept this data-type. We recommend all raw sequencing data be deposited in a public repository such as NCBI.
- Map, marker, QTL, and GWAS
- Please see the table below for links to templates and guides to the needed information.
- Genotype, phenotype, and/or haplotype data from cultivar/breeding line evaluation projects
- We will host genotype, phenotype, and/or haplotype data from cultivar, breeding line, and accessions with primary research importance. Please provide data in appropriate templates that can be downloaded below. SNP genotype data can also be provided in VCF. Phenotype and/or genotype data of progeny poputlations and panels will be made available for download.
Data templates
Below are the data templates in column 1 and the data types in the remaining columns. Each row indicates which templates are needed/required for each data type. The templates are downloaded by clicking the template name. We recommend you contact us before filling in the template so that we can work closely with you to ensure this process is expedited easily and quickly. Use ORCID for contact column and DOI for reference column in every sheet.
*when there are genome position data for markers and/or QTLs, provide the data in genome_position template
| Template | Marker | Genetic Map | QTL | GWAS | Genotype | Haplotype | Phenotype |
|---|---|---|---|---|---|---|---|
| Marker | Required | Required | May need | Required | Required | Required | |
| Genome Position | May need | May need | May need | May need | May need | ||
| Stock | Required | Required | May need | Required | Required | Required | |
| Map | Required | May need | |||||
| Map Position | Required | May need | |||||
| Dataset | Required | Required | Required | Required | Required | ||
| Trait | Required |
Required |
Required | ||||
| QTL | Required | ||||||
| MTL | May need | May need | |||||
| Descriptor | May need | Required | Required | ||||
| QTL Trait Data | May need | ||||||
| GWAS | Required | ||||||
| GWAS trait data | May need | ||||||
| GWAS group | May need | ||||||
|
Genotype |
Form 1 or Form 2 or Form 3 or VCF |
||||||
| Haplotype | Required | ||||||
| Haplotype block | Required | ||||||
| Haplotype SNP | Required | ||||||
| Phenotype | Required |