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Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander

Song, Xiaoming, Nie, Fulei, Chen, Wei, Ma, Xiao, Gong, Ke, Yang, Qihang, Wang, Jinpeng, Li, Nan, Sun, Pengchuan, Pei, Qiaoying, Yu, Tong, Hu, Jingjing, Li, Xinyu, Wu, Tong, Feng, Shuyan, Li, Xiu-Qing, Wang, Xiyin·2020·Horticulture Research
DOI 10.1038/s41438-020-0261-0PMC PMC7109041
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Abstract

Coriander (Coriandrum sativum L.), also known as cilantro, is a globally important vegetable and spice crop. Its genome and that of carrot are models for studying the evolution of the Apiaceae family. Here, we developed the Coriander Genomics Database (CGDB, http://cgdb.bio2db.com/) to collect, store, and integrate the genomic, transcriptomic, metabolic, functional annotation, and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants. Using these data sets in the CGDB, we intriguingly found that seven transcription factor (TF) families showed significantly greater numbers of members in the coriander genome than in the carrot genome. The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15, followed by those for tubby protein (TUB) and heat shock factors. As a demonstration of CGDB applications, we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses. RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander. CGDB allows bulk downloading, significance searches, genome browser analyses, and BLAST searches for comparisons between coriander and other plants regarding genomics, gene families, gene collinearity, gene expression, and the metabolome. A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions. CGDB will be continuously updated, and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.

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Crossref · 10.1038/s41438-020-0261-0

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Fig. 1 Flowchart of the Coriander Genomics Database (CGDB) sitemap
Fig. 1 Flowchart of the Coriander Genomics Database (CGDB) sitemapCC BY · PubMed Central
Fig. 2 The architecture of the Coriander Genomics Database (CGDB) mainly includes the home, browse, search, tools, download, help, and contact modules
Fig. 2 The architecture of the Coriander Genomics Database (CGDB) mainly includes the home, browse, search, tools, download, help, and contact modulesCC BY · PubMed Central
Fig. 3 The main functions of the browse and search module. a Home page. b Gene annotation page. c Gene family browser page. d Transcriptome data search page. e Metabolome data search page
Fig. 3 The main functions of the browse and search module. a Home page. b Gene annotation page. c Gene family browser page. d Transcriptome data search page. e Metabolome data search pageCC BY · PubMed Central
Fig. 4 Gene synteny search function of CGDB. a A search for syntenic genes. b A search for figures illustrating synteny
Fig. 4 Gene synteny search function of CGDB. a A search for syntenic genes. b A search for figures illustrating syntenyCC BY · PubMed Central
Fig. 5 Transcription factor (TF) analyses of coriander and carrot genomes. a The number of members of each TF family in these two species. Green represents coriander, and orange represents carrot. b The TFs showing the 12 highest ratios of the number in coriander to that in carrot
Fig. 5 Transcription factor (TF) analyses of coriander and carrot genomes. a The number of members of each TF family in these two species. Green represents coriander, and orange represents carrot. b The TFs showing the 12 highest ratios of the number in coriander to that in carrotCC BY · PubMed Central
Fig. 6 TUB gene family analyses. a The evolution and divergence time of grape, carrot, and coriander. b Phylogenetic tree constructed using the TUB family genes of these three species. The tree was divided into nine groups, from A to I. The numbers in parentheses represent the number of genes lost in coriander and carrot, respectively. c TUB family gene expression analyses of the coriander and carrot genomes at 30, 60, and 90 days after sowing. The FPKM values of gene expression were transformed by log2
Fig. 6 TUB gene family analyses. a The evolution and divergence time of grape, carrot, and coriander. b Phylogenetic tree constructed using the TUB family genes of these three species. The tree was divided into nine groups, from A to I. The numbers in parentheses represent the number of genes lost in coriander and carrot, respectively. c TUB family gene expression analyses of the coriander and carrot genomes at 30, 60, and 90 days after sowing. The FPKM values of gene expression were transformed by log2CC BY · PubMed Central

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Research works printed but not linked: 18

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Cited by

Metadata

Authors
Song, X., Nie, F., Chen, W., Ma, X., Gong, K., Yang, Q., Wang, J., Li, N., Sun, P., Pei, Q., Yu, T., Hu, J., Li, X., Wu, T., Feng, S., Li, X.-Q., & Wang, X.
ORCID
Venue
Horticulture Research
Publisher
Oxford University Press (OUP)
Published
2020-04-01
Volume
7
Issue
1
ISSN
  • 2662-6810
  • 2052-7276
DOI
10.1038/s41438-020-0261-0
PMC
PMC7109041
Cited by
56
References
0
Language
en
Licence
Funders
China-Hebei 100 Scholars Supporting Project to

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