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A Genomic, Transcriptomic, and Metabolic Database for Coriander

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A Genomic, Transcriptomic, and Metabolic Database for Coriander Song et al. Horticulture Research (2020) 7:55 Horticulture Research https://doi.org/10.1038/s41438-020-0261-0 www.nature.com/hortres ARTICLE Open Access Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander Xiaoming Song1, Fulei Nie1, Wei Chen1,2,XiaoMa3,KeGong1, Qihang Yang1, Jinpeng Wang 1, Nan Li1, Pengchuan Sun 1, Qiaoying Pei1, Tong Yu1, Jingjing Hu1,XinyuLi1,TongWu1,ShuyanFeng1, Xiu-Qing Li4 and Xiyin Wang 1,2 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 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; 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. Introduction carrot (Daucus carota) and celery (Apium graveolens). Coriandrum sativum L. (2n = 2× = 22) is an Apiaceae Coriander is a globally important vegetable crop. Its species whose young plants before flowering are usually production tripled from 1994 to 2016, and Asia accounts referred to as cilantro or Chinese parsley, whereas its for 71.4% of its total production worldwide (http:// flowering plants and seeds are generally referred to as faostat3.fao.org/). coriander. The Apiaceae family exhibits more than Coriander exhibits high nutrient levels, and is rich in 3700 species in 434 genera (https://en.wikipedia.org/wiki/ vitamin C and carotene1. Coriander leaves and stems are Apiaceae), including several well-known crops such as edible vegetables, and its seeds can be used as a spice. In addition, coriander contains several medicinal ingredients and presents important medicinal value. Interestingly, Correspondence: Xiyin Wang ([email protected]) 1Center for Genomics and Biocomputing/College of Life Sciences, North China Coriander contains many volatile oils that are responsible University of Science and Technology, Tangshan, Hebei 063210, China for its special aroma, which arouses an unpleasant reac- 2 School of Genomics and Bio-Big-Data, Chengdu University of Traditional tion in 4–14% of people (https://en.wikipedia.org/wiki/ Chinese Medicine, Chengdu 610075, China Full list of author information is available at the end of the article Coriander). Scientists have found that most people who The authors contributed equally: Xiaoming Song, Fulei Nie, Wei Chen © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a linktotheCreativeCommons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Song et al. Horticulture Research (2020) 7:55 Page 2 of 10 dislike coriander share a common olfactory receptor gene, Table 1 Summary of main genome databases for OR6A2, whose product absorbs the odor of aldehyde genome-sequenced plants 2 chemicals . Species Database Links With the rapid development of sequencing technolo- gies, an increasing number of genomes are being Arabidopsis TAIR http://www.arabidopsis.org/index.jsp 3,4 Rice RGAP http://rice.plantbiology.msu.edu sequenced and released . Therefore, many plant genome Maize MaizeGDB https://www.maizegdb.org databases have been constructed to allow researchers to Soybean SoyBase https://soybase.org search and download omics data sets. Although these Apple AppleGFDB http://gfdb.sdau.edu.cn statistics are incomplete, there are more than 40 available Cacao CGD https://www.cacaogenomedb.org/main genome databases for single plants or families such as Pineapple PGD http://pineapple.angiosperms.org/ pineapple/html/index.html Arabidopsis (http://www.arabidopsis.org/index.jsp), rice Cabbage Bolbase http://ocri-genomics.org/bolbase/ (http://rice.plantbiology.msu.edu), maize (https://www. Carrot CarrotDB http://apiaceae.njau.edu.cn/carrotdb 5 6 7 8 maizegdb.org) , cotton , carrot , Chinese cabbage , pine- Peanut PeanutBase https://www.peanutbase.org 9 10 apple , and strawberry (Table 1). In comparison with Wheat ATGSP http://aegilops.wheat.ucdavis.edu/ATGSP/ other families, few genome sequences have been released Pepper PGP http://peppergenome.snu.ac.kr for the Apiaceae family, and only the carrot genome has Quinoa QGDB http://quinoa.kazusa.or.jp been sequenced thus far11. However, there is no such Chrysanthemum CGDB http://www.amwayabrc.com Chickpea CGAP http://www.nipgr.ac.in/CGAP/home.php database available for coriander, which limits the ability of Citrus CAP http://citrus.hzau.edu.cn/orange/ researchers to obtain genomic and other types of omics Cucurbit CuGenDB http://cucurbitgenomics.org data for coriander. Although a carrot genome database Carnation Carnation DB http://carnation.kazusa.or.jp has been built, the genome size, gene number, and Eucalyptus ECDB http://www.kazusa.or.jp/eucaly/ number of repeat sequences are significantly greater in Strawberry GARDEN http://strawberry-garden.kazusa.or.jp coriander than in carrot. Therefore, it is necessary to build Sunflower SGDB https://sunflowergenome.org a genome data analysis platform for coriander together Sweetpotato GARDEN http://sweetpotato-garden.kazusa.or.jp Morning glory INGP http://viewer.shigen.info/asagao/ with carrot genome data. Cotton CottonGen https://www.cottongen.org Here, we report the construction of the Coriander Hop HopBase http://hopbase.cgrb.oregonstate.edu Genomics Database (CGDB), which contains a high- Jatropha JGDB https://www.kazusa.or.jp/jatropha/ quality genome assembly of coriander obtained with the Lettuce LGR http://lgr.genomecenter.ucdavis.edu most recent sequencing technologies and novel bioinfor- Medicago MGD http://www.medicagogenome.org Mint MGR http://langelabtools.wsu.edu/mgr/ matics methods. Moreover, this database contains RNA- organism/Mentha/longifolia seq and metabolic data sets from four tissues and three Banana BGH https://banana-genome-hub.southgreen.fr periods for coriander and carrot. The CGDB also provides Zoysia ZGD http://zoysia.kazusa.or.jp a large amount of comparative genomic analysis data, Panax PNGD http://www.plantkingdomgdb.com/ such as information on collinear blocks, transcription panax_notoginseng/ Oak OGS http://www.oakgenome.fr factors, repeat sequences, and gene annotations. All users Radish RGD http://radish.kazusa.or.jp can readily access the data using the browser and query a Eggplant EGDB http://eggplant.kazusa.or.jp variety of data types from the CGDB, including genomic, Pennycress PG http://pennycress.umn.edu annotation, TF, RNA-seq, and metabolic data sets. We Vangularis VIGGS https://viggs.dna.affrc.go.jp hope that CGDB will become an important platform for Brassica BRAD http://brassicadb.org/brad/ the plant research community to conduct comparative Rosaceae GDR https://www.rosaceae.org and functional genomic analyses of coriander and other Gramene Gramene http://www.gramene.org Solanaceae SGN https://solgenomics.net related plants. Materials and methods Collection of genome, expression, and metabolic data sets genes from coriander and carrot from three different The genomic, expression, and metabolic data sets growth stages. All the analysis results for these data sets included in our CGDB database were obtained from are easily navigable and available in the CGDB. standard experiments and bioinformatics analyses. The genomic data sets mainly contained genome sequence, Transcription factor family identification gene sequence, protein sequence, gff, gene annotation, Transcription factors (TFs) play very important roles in and repeat sequence data. The expression data sets mainly regulating the expression
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