Table 3 List of horticultural plant-centric genome databases

From: Genome sequences of horticultural plants: past, present, and future

Database name	Covered species	Tools
Herbal Medicine Omics Database	Calotropis gigantea	BLAST
(herbalplant.ynau.edu.cn)	Catharanthus roseus	GBrowse
	Rhodiola rosea
	Gastrodia elata
	Eucommia ulmoides
	Camptotheca acuminata
	Ginkgo biloba
	Dioscorea rotundata
	Panax ginseng
	Punica granatum
	Boea hygrometrica
	Jatropha curcas
	Glycyrrhiza uralensis
	Cannabis sativa
	Macleaya cordata
	Mentha longifoli
	Erigeron breviscapus
	Panax notoginseng
	Moringa oleifera
	Lepidium meyenii
	Dendrobium officinale
	Salvia miltiorrhiza
Genome Database for Rosaceae (GDR)	Fragaria vesca	Breeding Information Management System
(www.rosaceae.org)	Fragaria x ananassa	BLAST+
	Malus x domestica	Breeders Toolbox
	Prunus armeniaca	GDRCyc
	Prunus avium	JBrowse
	Prunus cerasus	MapViewer
	Prunus dulcis	Pathway Inspector
	Prunus persica	Primer3
	Prunus serotina	Sequence Retrieval
	Pyrus communis	Synteny Viewer
	Rubus occidentalis
Sol Genomics Network	Solanum pennellii	BLAST
(solgenomics.net)	Solanum lycopersicoides	VIGS Tool
	Nicotiana attenuata	Alignment Analyzer
	Nicotiana benthamiana	Tree Browser
	Nicotiana tabacum	Genome Browser (JBrowse)
	Petunia axillaris	Comparative Map Viewer
	Petunia inflata	CAPS Designer
	Solanum pimpinellifolium	solQTL: QTL Mapping
	Solanum lycopersicum	In Silico PCR
	Solanum tuberosum	Tomato Expression Atlas (TEA)
	Solanum phureja	Tomato Expression Database (TED)
	Capsicum annuum	SolCyc Biochemical Pathways
	Petunia axillaris	Coffee Interactomic Data
	Petunia x hybrida	SGN Ontology Browser
	Petunia integrifolia var inflata	Breeders Toolbox
		FTP Site
		Download Gene Sequences
		Clones, Arrays, Unigenes and BACs
		Unigene Converter
Citrus Genome Database (CGD)	Citrus clementina	Breeding Information Management System
(www.citrusgenomedb.org)	Citrus ichangensis	BLAST+
	Citrus sinensis	Breeders Toolbox
	Citrus reticulata	GDRCyc
	Citrus maxima	JBrowse
	Citrus medica	MapViewer
	Poncirus trifoliata	Pathway Inspector
	Atalantia buxifolia	Primer3
		Sequence Retrieval
		Synteny Viewer
Cool Season Food Legume Database (CSFL)	Cicer arietinum	JBrowse
(www.coolseasonfoodlegume.org)	Cicer reticulatum	PathwayCyc
	Vicia faba	Breeding Information Management System
	Pisum sativum	MapViewer
	Lens culinaris	Synteny Viewer
		BLAST+
Cucurbit Genomics Database (CuGenDB)	Cucumis sativus	BLAST
(cucurbitgenomics.org)	Cucumis melo	JBrowse
	Citrullus lanatus	Batch Query
	Cucurbita maxima	Synteny Viewer
	Cucurbita moschata	CMAP
	Cucurbita pepo	CucurbitCyc
	Lagenaria siceraria	Pathway enrichment
		GO enrichment
		Gene classification
Banana Genome Hub	Musa acuminata DH-Pahang	BLAST
(banana-genome-hub.southgreen.fr)	Musa acuminata Banksii	JBrowse
	Musa acuminata Zebrina	GBrowser
	Musa acuminata Calcutta 4	Generic Maps
	Musa balbisiana PKW	Gene Family
	Musa Itinerans	Chromosome viewer
	Musa schizocarpa	Transcriptomic Search
		Design primer
		Ontology Browser
		Dotplot
Brassica database (BRAD)	Brassica rapa	BLAST
(brassicadb.org)	Brassica juncea	Gbrowse
	Brassica napus	Markers and Maps
	Brassica oleracea	Gene families
		Glucosinolate genes
		Anthocyanin genes
		Resistance genes
		Flower genes
		Transcription factors
		Auxin genes
		Phenotypes
		People/Labs
Pepper Pangenome Browser (PepperPan)	Capsicum annuum	Generic genome browser
(www.pepperpan.org:8012)	Capsicum baccatum
	Capsicum frutescens
Cofffee Genome Hub (CGH)	Coffea canephora	Advanced Search
(www.coffee-genome.org/coffeacanephora)	Coffea arabica	Chromosome Viewer
		Gene annotation
		Gene Expression
		Gene Families
		Genetic Map
		Primer Blaster
		Primer Designer
		SNPs
		Blast
		JBrowse
		GBrowser
Viggs	Vigna marina subsp. oblonga	Gbrowse
(viggs.dna.affrc.go.jp)	Vigna angularis	BLAST
	Vigna angularis (Willd.)	BLAT
	Vigna vexillata
Cannabis genome project (CCBR)	Cannabis sativa	BLAST
(genome.ccbr.utoronto.ca/cgi-bin/hgGateway)		GBrowser
		Design primer
Carnation DB	Dianthus caryophyllus	BLAST
(carnation.kazusa.or.jp)
HopBase	Humulus lupulus	BLAST
(hopbase.cgrb.oregonstate.edu)		Gbrowse
Medicago truncatula Genome Database (MTGD)	Medicago truncatula	JBrowse
(www.medicagogenome.org)		BLAST
		Web Services
		CMap (LegumeInfo.org)
		GO Analysis
		InterPro Annotations
Tea Plant Information Archive (TPIA)	Camellia sinensis	BLAST
(tpia.teaplant.org/)		Gbrowse
		Pathway
		Correlation Analysis
		Function Erichment
		Batch Retrival
Mulberry Genome Database (MorusDB)	Morus notabilis	Transposable Element Analysis
(morus.swu.edu.cn/morusdb)		Horizontal Gene Transfer Analysis
		Ortholog and Paralog Group Analysis
		BLAST
		WEGO
		HMMER
		Browse GO
		Search GO
		Find Motifs
Pear Genome Project	Pyrus bretschneideri	Download
(peargenome.njau.edu.cn)
Radish Genome database	Raphanus sativus	BLAST
(www.radish-genome.org/)		Gbrowse
		Expression
CsiDB	Citrus sinensis	Gene Search
(citrus.hzau.edu.cn)		BLAST
		GBrowser
		PPI
		Pathway
Mint Genomics Resource	Mentha longifolia	BLAST
(langelabtools.wsu.edu/mgr/organism/Mentha/longifolia)		Gbrowse
		Pathway
CeleryDB	Apium graveolens	BLAST
(apiaceae.njau.edu.cn)		GBrowser
		Transcription factors
CarrotDB	Daucus carota	BLAST
(apiaceae.njau.edu.cn/)		Gbrowse
		Transcription factors
		Germplasm Resources Collection
Banana Genome Hub	Musa acuminata DH-Pahang	BLAST
(banana-genome-hub.southgreen.fr)	Musa acuminata Banksii	JBrowse
	Musa acuminata Zebrina	GBrowser
	Musa acuminata Calcutta 4	Generic Maps
	Musa balbisiana PKW	Gene Family
	Musa Itinerans	Chromosome viewer
	Musa schizocarpa	Transcriptomic Search
		Design primer
		Ontology Browser
		Dotplot
Brassica database (BRAD)	Brassica rapa	BLAST
(brassicadb.org)	Brassica juncea	Gbrowse
	Brassica napus	Markers and Maps
	Brassica oleracea	Gene families
		Glucosinolate genes
		Anthocyanin genes
		Resistance genes
		Flower genes
		Transcription factors
		Auxin genes
		Phenotypes
		People/Labs
Pepper Pangenome Browser (PepperPan)	Capsicum annuum	Generic genome browser
(www.pepperpan.org:8012)	Capsicum baccatum
	Capsicum frutescens
Cofffee Genome Hub (CGH)	Coffea canephora	Advanced Search
(www.coffee-genome.org/coffeacanephora)	Coffea arabica	Chromosome Viewer
		Gene annotation
		Gene Expression
		Gene Families
		Genetic Map
		Primer Blaster
		Primer Designer
		SNPs
		Blast
		JBrowse
		GBrowser
Viggs	Vigna marina subsp. oblonga	Gbrowse
(viggs.dna.affrc.go.jp)	Vigna angularis	BLAST
	Vigna angularis (Willd.)	BLAT
	Vigna vexillata
Cannabis genome project (CCBR)	Cannabis sativa	BLAST
(genome.ccbr.utoronto.ca/cgi-bin/hgGateway)		GBrowser
		Design primer
Carnation DB	Dianthus caryophyllus	BLAST
(carnation.kazusa.or.jp)
HopBase	Humulus lupulus	BLAST
(hopbase.cgrb.oregonstate.edu)		Gbrowse
Medicago truncatula Genome Database (MTGD)	Medicago truncatula	JBrowse
(www.medicagogenome.org)		BLAST
		Web Services
		CMap (LegumeInfo.org)
		GO Analysis
		InterPro Annotations
Tea Plant Information Archive (TPIA)	Camellia sinensis	BLAST
(tpia.teaplant.org/)		Gbrowse
		Pathway
		Correlation Analysis
		Function Erichment
		Batch Retrival
Mulberry Genome Database (MorusDB)	Morus notabilis	Transposable Element Analysis
(morus.swu.edu.cn/morusdb)		Horizontal Gene Transfer Analysis
		Ortholog and Paralog Group Analysis
		BLAST
		WEGO
		HMMER
		Browse GO
		Search GO
		Find Motifs
Pear Genome Project	Pyrus bretschneideri	Download
(peargenome.njau.edu.cn)
Radish Genome database	Raphanus sativus	BLAST
(www.radish-genome.org/)		Gbrowse
		Expression
CsiDB	Citrus sinensis	Gene Search
(citrus.hzau.edu.cn)		BLAST
		GBrowser
		PPI
		Pathway
Mint Genomics Resource	Mentha longifolia	BLAST
(langelabtools.wsu.edu/mgr/organism/Mentha/longifolia)		Gbrowse
		Pathway
CeleryDB	Apium graveolens	BLAST
(apiaceae.njau.edu.cn)		GBrowser
		Transcription factors
CarrotDB	Daucus carota	BLAST
(apiaceae.njau.edu.cn/)		Gbrowse
		Transcription factors
		Germplasm Resources Collection

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