Tropical Crop Omics Database is a data resource serving the research on selective breeding and trait improvement of tropical crops. By integrating multi-omics data from five species including cassava, rubber tree, sugarcane, mango and pineapple, TCOD provides eight module (species, projects, samples, publications, genomes, variations, genes and cultivars) to browse and analyze. Meanwhile, TCOD also embeds the genome browser and blast tools.

1. Projects

Projects module collected all projects used for variant analysis. Users can preform advanced searches based on project ID, SRA accession, year, submitter, organism and so on. The detailed sample information and runs information contained in each project can be viewed by clicking the hyperlink.

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2. Samples

Samples module collected all samples used for variant analysis. Users can preform advanced searches based on sample ID, SRA accession, sample name, country, provider and so on. The detailed runs information contained in each sample can be viewed by clicking the hyperlink. At the same time, variant files (GVCF/VCF) for each sample can also be downloaded directly.

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3. Publications

The literature in publication module is from NGDC OpenLB, which is updated in real time. The main contents include three parts:

  • The list of publications
  • Statistics of the number of papers published each year, once you click on the legend, the list of publications will be filled with the literature information of the corresponding year
  • Statistics on the proportion of published journals, once you click on the legend, the list of publications will be filled with the literature information of the corresponding journal

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4. Genomes

The assembly level of the genome sequences collected by the genome module reaches the chromosome level, which can provide users with good data support. The main contents include three parts:

  • The basic information of each genome
  • The detail information of each chromosome in the genome
  • The idiogram of each genome, from the idiogram, we can see how genes are distributed across the whole genome. While click one of the chromosome, we can jump to the visualization interface of each chromosome

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5. Variations

Variations module provides genome-wide variation maps for 4 species, including cassava, rubber tree, mango, and pineapple. The pipeline of variation analysis can refer to NGDC GVM database. The main contents include three parts:

  • Distribution of variants in each chromosome
  • The list of variants, once you click the variants ID, you can view the basic information, the annotation information and the distribution of genotype among different populations
  • Advanced search, we can filter variants according to variant ID, position, consequence type, minor allele frequency, gene name and so on

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6. Genes

Genes module collects gene information from all genomes, and supports multi-condition advanced search. The main contents of each gene include:

  • Basic information: such as position, structure and function annotation of the gene
  • Gene sequence: including nucleotide sequence and protein sequence
  • The variants list, if there are variants in the gene
  • Visualization within gene regions

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7. Cultivars

Cultivars module only includes cassava germplasm items at present, the main source websites are CIAT and IITA. In this module, we can view the global distribution of collected cassava varieties. The main contents of each variety include:

  • Basic information, such as accession ID, cultivar name, country of origin, altitude, latitude and longitude
  • Botanical characteristics, such as the height of plant, the shape of leaf, the color of leaf and so on
  • Agronomic characteristics, such as the shape of root, the color of root, dry matter content and so on

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