OrangeExpDB-The Orange expression database

OrangeExpDB is an online Citrus transcriptome database that provides expression data for a variety of Citrus RNA-seq samples, including 9 Citrus limon projects, 18 Citrus reticulata projects, 56 Citrus sinensis projects, 14 Citrus trifoliata projects and 26 Citrus maxima projects. Additionally, the platform also offers practical tools such as online blast, search function, and download tools, thus furnishing a convenient and reliable research foundation for researchers.

Note: Raw data from the NCBI-SRA database was subjected to quality control using Trimmomatic v0.39. Subsequently, Hisat2 v2.2.1 and StringTie v2.2.1 were used to calculate the fragments per kilobase of transcript per million mapped reads (FPKM) matrices.

BioProject	Publication	Bytes	geo_loc_name_country_continent	geo_loc_name_country	geo_loc_name
PRJNA894942	Nanopore long-read RNAseq reveals transcriptional variations in citrus species	1.85 Gb	Asia	China	China
PRJNA847378	Bidirectional mRNA transfer between Cuscuta australis and its hosts	5.64 Gb	Asia	China	China
PRJNA836261	Suppression of citrus canker disease mediated by flagellin perception	17.79 Gb	not applicable	not applicable	not applicable
PRJNA827341	The plant protection preparation GZM improves crop immunity, yield, and quality	13.03 Gb	Asia	China	China:Guangdong
PRJNA797721	An effector of ‘Candidatus Liberibacter asiaticus’ manipulates autophagy to promote bacterial infection	22.15 Gb	Asia	China	China:Chongqing
PRJNA735893	A chromosome-level phased Citrus sinensis genome facilitates understanding Huanglongbing tolerance mechanisms at the allelic level in an irradiation-induced mutant	74.48 Gb	North America	USA	USA: Florida
PRJNA792482	-	40.84 Gb	Asia	China	China:Jiangxi
PRJNA778304	miR156 regulates somatic embryogenesis by modulating starch accumulation in citrus	42.44 Gb	North America	USA	USA: Lake Alfred, FL
PRJNA780217	Citrus Huanglongbing is a pathogen-triggered immune disease that can be mitigated with antioxidants and gibberellin	14.65 Gb	North America	USA	USA: Florida
PRJNA778232	Volatile Signals From Guava Plants Prime Defense Signaling and Increase Jasmonate-Dependent Herbivore Resistance in Neighboring Citrus Plants	24.66 Gb	Asia	China	China: Guangzhou
PRJNA755969	Insights into the mechanism of Huanglongbing tolerance in the Australian finger lime (Citrus australasica)	11.1 Gb	North America	USA	USA: Florida
PRJNA755699	Overexpression of the salicylic acid binding protein 2 (SABP2) from tobacco enhances tolerance against Huanglongbing in transgenic citrus	27.62 Gb	North America	USA	USA: Florida
PRJNA752966	-	21.33 Gb	Asia	China	China:Jiangxi Province
PRJNA748945	Transcriptomic Analysis of the Host Response to Mild and Severe CTV Strains in Naturally Infected Citrus sinensis Orchards	3.74 Gb	North America	Mexico	Mexico: Veracruz
PRJNA741128	Transcriptomic and physiological analysis reveals interplay between salicylic acid and drought stress in citrus tree floral initiation	56.25 Gb	Asia	China	China:Wuhan
PRJNA723633	-	14.26 Gb	Asia	China	China: Chongqing
PRJNA715742	-	39.45 Gb	North America	USA	USA: Riverside, CA
PRJNA704425	-	6.95 Gb	North America	USA	USA: Riverside, CA
PRJNA703546	-	264.08 Gb	-	-	-
PRJNA612768	Natural variations of TFIIAγ gene and LOB1 promoter contribute to citrus canker disease resistance in Atalantia buxifolia	53.55 Gb	Asia	China	China
PRJNA691971	-	31.49 Gb	Asia	China	China: Hubei Province
PRJNA689213	Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation	86.05 Gb	-	-	-
PRJNA670516	CsLOB1 regulates susceptibility to citrus canker through promoting cell proliferation in citrus	42.97 Gb	Asia	China	China
PRJNA667275	Transcription factor WRKY22 regulates canker susceptibility in sweet orange (Citrus sinensis Osbeck) by enhancing cell enlargement and CsLOB1 expression	25.46 Gb	Asia	China	China:Chongqing
PRJNA647249	Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq	36.5 Gb	Asia	China	China:Fuzhou
PRJNA642106	-	11.78 Gb	-	-	-
PRJNA636131	Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel Orange	32.41 Gb	Asia	China	China:Wuhan
PRJNA629966	-	26.58 Gb	-	-	-
PRJNA602381	Potential Mechanisms of AtNPR1 Mediated Resistance against Huanglongbing (HLB) in Citrus	21.97 Gb	North America	USA	USA: Florida
PRJNA597410	Lycopene Accumulation in Cara Cara Red-flesh Navel Orange Is Correlated with Weak Abscisic Acid Catabolism	16.07 Gb	Asia	China	China:Wuhan
PRJNA579049	Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers	13.29 Gb	Asia	China	China
PRJNA573296	Regulation of carotenoid and chlorophyll pools in hesperidia, anatomically unique fruits found only in Citrus	93.42 Gb	Asia	China	China: hubei
PRJNA576978	Overexpressing GH3.1 and GH3.1L reduces susceptibility to Xanthomonas citri subsp	16.87 Gb	Asia	China	China: Chongqing
PRJNA566421	Assessment of unconventional antimicrobial compounds for the control of 'Candidatus Liberibacter asiaticus', the causative agent of citrus greening disease	158.91 Gb	-	-	-
PRJNA513165	"Instituto Nacional de Ciência e Tecnologia de Genômica para o Melhoramento de Citros" (Grant ID 2008/2014/50880-0, Fundação de Amparo à Pesquisa do Estado de São Paulo) "Instituto Nacional de Ciência e Tecnologia de Genômica para o Melhoramento de Citros" (Grant ID 465440/2014-2, Conselho Nacional de Desenvolvimento Científico e Tecnológico) "Relações hídricas e transcriptoma comparativo de porta-enxertos selecionados pelo programa de melhoramento genético de citros visando tolerância à seca" (Grant ID 478733/2013-5, Conselho Nacional de Desenvolvimento Científico e Tecnológico)	11.69 Gb	South America	Brazil	Brazil: Ilheus
PRJNA508424	-	14.87 Gb	Asia	China	China: chongqing
PRJNA505360	Functional analysis of citrus AP2 transcription factors identified CsAP2-09 involved in citrus canker disease response and tolerance	8.42 Gb	Asia	China	China: chongqing
PRJNA488876	-	35.87 Gb	Asia	China	China
PRJNA340305	Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction	55.62 Gb	Asia	China	China
PRJNA471083	Molecular and Physiological Responses of Citrus sinensis Leaves to Long-Term Low pH Revealed by RNA-Seq Integrated with Targeted Metabolomics Low pH-responsive proteins revealed by a 2-DE based MS approach and related physiological responses in Citrus leaves	13.54 Gb	-	-	-
PRJNA417324	"National Institute of Food and Agriculture Hatch Project" (Grant ID 1005945, United States Department of Agriculture) "HLB Early Detection" (Grant ID 5300-150, Citrus Research Board)	87.12 Gb	North America	USA	USA:Davis
PRJNA429187	Global increase in DNA methylation during orange fruit development and ripening	49.27 Gb	-	-	-
PRJNA428949	Transcriptomic Analysis of Orange Fruit Treated with Pomegranate Peel Extract (PGE)	29.35 Gb	Europe	Italy	Italy: Reggio Calabria
PRJNA428873	Genome-wide identification, characterization, and expression profile of NBS-LRR gene family in sweet orange (Citrus sinensis)	11.72 Gb	-	-	-
PRJNA394061	Comparative analysis of the transcriptomes of the calyx abscission zone of sweet orange insights into the Huanglongbing-associated fruit abscission	51.04 Gb	-	-	-
PRJNA384780	Transcriptional analysis of sweet orange trees co-infected with ‘Candidatus Liberibacter asiaticus’ and mild or severe strains of Citrus tristeza virus	58.33 Gb	North America	USA	USA:MD,Beltsville
PRJNA387319	Comparative transcriptome and proteome profiling of two Citrus sinensis cultivars during fruit development and ripening	54.45 Gb	Asia	China	China:Xindu district,Chengdu
PRJNA350382	-	11.41 Gb	Asia	China	China
PRJNA339838	Root Adaptive Responses to Aluminum-Treatment Revealed by RNA-Seq in Two Citrus Species With Different Aluminum-Tolerance	4.69 Gb	-	-	-
PRJEB6342	An RNA-Seq-based reference transcriptome for Citrus	5.49 Gb	-	-	-
PRJNA304618	-	8.71 Gb	North America	USA	USA
PRJNA299762	-	4.66 Gb	Asia	China	China:Ganzhou
PRJNA261357	Transcriptional profile of sweet orange in response to chitosan and salicylic acid	11.63 Gb	uncalculated	uncalculated	missing
PRJNA203307	Published online, DOI: Transcriptome Profiling of Citrus Fruit Response to Huanglongbing Disease Published online, DOI: Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms	35.39 Gb	North America	USA	USA:Florida, Lake Alfred
PRJNA839431	Reduction of heat stress pressure and activation of photosystem II repairing system are crucial for citrus tolerance to multiple abiotic stress combination	113.17 Gb	-	-	-

BioProject	Publication	Bytes	geo_loc_name_country_continent	geo_loc_name_country	geo_loc_name
PRJNA838230	Transcriptome analysis of Citrus limon infected with Citrus yellow vein clearing virus	12.33 Gb	Asia	China	China: Chongqing
PRJNA812325	A gap-free and haplotype-resolved lemon genome provides insights into flavor synthesis and huanglongbing (HLB) tolerance	18.48 Gb	Asia	China	China:Guangxi
PRJNA716747	Transcriptome and Metabolome Comparison of Smooth and Rough Citrus limon L. Peels Grown on Same Trees and Harvested in Different Seasons	51.89 Gb	Asia	China	China:Baoshan
PRJNA606613	Exploring the differential stages of the pigment metabolism by pre-harvest bagging and post-harvest ethylene de-greening of Eureka lemon peel	51.89 Gb	18.41 Gb	Asia	China	China:Sichuan
PRJNA532796	Unravelling lncRNA mediated gene expression as potential mechanism for regulating secondary metabolism in Citrus limon	48.74 Gb	Asia	China	China:Chengdu
PRJNA355134	Identification of Genes Associated with Lemon Floral Transition and Flower Development during Floral Inductive Water Deficits: A Hypothetical Model.	24.20 Gb	18.73 Gb	not applicable	not applicable	not applicable
PRJNA348468	Longitudinal Transcriptomic, Proteomic, and Metabolomic Analysis of Citrus limon Response to Graft Inoculation by Candidatus Liberibacter asiaticus	24.20 Gb	North America	USA	USA: Davis
PRJEB6342	An RNA-Seq-based reference transcriptome for Citrus	13.37 Gb	not applicable	not applicable	not applicable

BioProject	Publication	Bytes	geo_loc_name_country_continent	geo_loc_name_country	geo_loc_name
PRJNA280255	Comparative Transcriptome and iTRAQ Proteome Analyses of Citrus Root Responses to Candidatus Liberibacter asiaticus Infection	12.34 Gb	not applicable	not applicable	not applicable
PRJNA300206	Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis	5.53 Gb	not applicable	not applicable	not applicable
PRJNA341756	Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction	40.72 Gb	Asia	China	China
PRJNA393070	-	43.81 Gb	Asia	China	China
PRJNA483477	Natural Variation in CCD4 Promoter Underpins Species-Specific Evolution of Red Coloration in Citrus Peel	24.11 Gb	Asia	China	China: Wuhan
PRJNA545864	Comparative analysis of the transcriptome, methylome, and metabolome during pollen abortion of a seedless citrus mutant	46.65 Gb	Asia	China	China:Wuhan
PRJNA623065	Transcriptome analysis of Chongyi wild mandarin, a wild species more cold-tolerant than Poncirus trifoliata, reveals key pathways in response to cold	25.02 Gb	Asia	China	China:Jiangxi
PRJNA640485	Restructuring citrus endophytic diversity through potential indigenous endophytes could eliminate huanglongbing pathogen Candidatus Liberibacter asiaticus	27.89 Gb	Asia	China	China
PRJNA645612	Integrative analyses of transcriptome and carotenoids profiling revealed molecular insight into variations in fruits color of Citrus Reticulata Blanco induced by transplantation	23.27 Gb	Asia	China	China:Guangxi
PRJNA706142	Transcriptomes and DNA methylomes in apomictic cells delineate nucellar embryogenesis initiation in citrus	56.26 Gb	Asia	China	China:Hubei
PRJNA734968	-	47.97 Gb	Asia	China	China: Hangzhou
PRJNA776912	CitWRKY28 and CitNAC029 promote the synthesis of cuticular wax by activating CitKCS gene expression in citrus fruit	29.73 Gb	Asia	China	China:Wuhan
PRJNA853264	Transcriptome analysis of the pulp of citrus fruitlets suggests that domestication enhanced growth processes and reduced chemical defenses increasing palatability	24.96 Gb	Europe	Spain	Spain: Valencia
PRJNA859629	-	36.94 Gb	Asia	China	China:Xinhui
PRJNA883800	Integrated Transcriptome and Metabolome Analysis Reveals Phenylpropanoid Biosynthesis and Phytohormone Signaling Contribute to "" Candidatus Liberibacter asiaticus"" Accumulation in Citrus Fruit Piths (Fluffy Albedo)	20.19 Gb	Asia	China	China
PRJNA885437	Comparative transcriptomic and metabolomic analyses reveal the delaying effect of naringin on postharvest decay in citrus fruit	18.45 Gb	Asia	China	China: Nanchang
PRJNA894942	Nanopore long-read RNAseq reveals transcriptional variations in citrus species	2.00 Gb	Asia	China	China

BioProject	Publication	Bytes	geo_loc_name_country_continent	geo_loc_name_country	geo_loc_name
PRJNA894942	Nanopore long-read RNAseq reveals transcriptional variations in citrus species	1.99 Gb	Asia	China	China
PRJNA820365	Integrated transcriptomic and metabolomic analyses reveal key genes controlling flavonoid biosynthesis in Citrus grandis ‘Tomentosa’ fruits	51.89 Gb	Asia	China	China: Huazhou
PRJNA817805	Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors during Fruit Development in Pomelo (Citrus maxima)	34.2 Gb	uncalculated	uncalculated	not collected
PRJNA796621	The high-quality genome of pummelo provides insights into the tissue-specific regulation of citric acid and anthocyanin during domestication	38.74 Gb	Asia	China	China:Jiangxi
PRJNA795605	-	17.61 Gb	Asia	China	China:Yunnan, Ruili
PRJNA776249	Acetylome reprograming participates in the establishment of fruit metabolism during polyploidization in citrus	14.86 Gb	Asia	China	China: Wuhan
PRJNA704217	Comparative transcriptomic analysis on compatible/incompatible grafts in Citrus	91.25 Gb	Asia	China	China:Sichuan
PRJNA683589	Integrated Analysis of Metabolome and Transcriptome Reveals the Difference in Flavonoid Biosynthesis between the Red- and White-Sarcocarp Pomelo Fruits	13.59 Gb	not applicable	not applicable	not applicable
PRJNA639316	-	17.73 Gb	uncalculated	uncalculated	not collected
PRJNA598932	Assembly of Satsuma mandarin mitochondrial genome and identification of cytoplasmic male sterility–specific ORFs in a somatic cybrid of pummelo	4.52 Gb	Asia	China	China:wuhan
PRJNA598773	Assembly of Satsuma mandarin mitochondrial genome and identification of cytoplasmic male sterility–specific ORFs in a somatic cybrid of pummelo	5.10 Gb	Asia	China	China:wuhan
PRJNA557834	Selection and Evaluation of a Thornless and HLB-Tolerant Bud-Sport of Pummelo Citrus With an Emphasis on Molecular Mechanisms	41.92 Gb	North America	USA	USA
PRJNA549576	Citrus mangshanensis Pollen Confers a Xenia Effect on Linalool Oxide Accumulation in Pummelo Fruit by Enhancing the Expression of a Cytochrome P450 78A7 Gene CitLO1	15.37 Gb	Asia	China	China:Wuhan
PRJNA526584	Evolution of self-compatibility by a mutant Sm-RNase in citrus	310.81 Gb	Asia	China	China
PRJNA488908	-	81.15 Gb	Asia	China	China:Jiangxi
PRJNA339650	Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction	82.49 Gb	Asia	China	China
PRJNA437176	Fruit characteristics, soluble sugar compositions and transcriptome analysis during the development of Citrus maxima “seedless”, and identification of SUS and INV genes involved in sucrose degradation	19.97 Gb	Asia	China	China:Hainan
PRJNA430310	-	18.48 Gb	Asia	China	China:,Fujian
PRJNA430306	-	16.84 Gb	Asia	China	China:,Fujian
PRJNA430145	-	15.62 Gb	Asia	China	China:,Fujian
PRJNA429973	-	17.02 Gb	Asia	China	China:,Fujian
PRJNA428873	Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis)	11.33 Gb	not applicable	not applicable	not applicable
PRJNA407231	-	16.4 Gb	Asia	China	China:Sichuan
PRJNA339838	Root Adaptive Responses to Aluminum-Treatment Revealed by RNA-Seq in Two Citrus Species With Different Aluminum-Tolerance	4.55 Gb	not applicable	not applicable	not applicable
PRJEB6342	An RNA-Seq-based reference transcriptome for Citrus	20.57 Gb	not applicable	not applicable	not applicable
PRJNA300206	Genome-scale mRNA and small RNA transcriptomic insights into initiation of citrus apomixis	5.82 Gb	not applicable	not applicable	not applicable
PRJNA271737	De novo transcriptome assembly of pummelo and molecular marker development	7.5G	Asia	China	China

BioProject	Publication	Bytes	geo_loc_name_country_continent	geo_loc_name_country	geo_loc_name
PRJNA934070	Integrated miRNA-mRNA analysis reveals candidate miRNA family regulating arbuscular mycorrhizal symbiosis of Poncirus trifoliata	33.23 Gb	Asia	China	China: Wuhan
PRJNA894942	Nanopore long-read RNAseq reveals transcriptional variations in citrus species	1.78 Gb	Asia	China	China
PRJNA487128	Evolutionary dynamics of linc RNA transcription in nine citrus species.	90.22 Gb	Asia	China	China
PRJNA587875	Identifying citrus CBL and CIPK gene families and their expressions in response to drought and arbuscular mycorrhizal fungi colonization	30.07 Gb	Asia	China	China:Jingzhou
PRJNA576788	Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency	36.17 Gb	not applicable	not applicable	not applicable
PRJNA558461	Transcriptome analysis reveals improved root hair growth in trifoliate orange seedlings by arbuscular mycorrhizal fungi	8.05 Gb	Asia	China	China:Hubei
PRJNA554373	-	8.38 Gb	Asia	China	China:Hubei
PRJNA482734	-	38.61 Gb	Asia	China	China: wuhan
PRJNA473568	Genome-wide comprehensive analysis of transcriptomes and small RNAs offers insights into the molecular mechanism of alkaline stress tolerance in a citrus rootstock	26.21 Gb	not applicable	not applicable	not applicable
PRJNA414000	Arbuscular Mycorrhizal Fungus Enhances Lateral Root Formation in Poncirus trifoliata (L.) as Revealed by RNA-Seq Analysis	13.3 Gb	Asia	China	China:Gaungzhou
PRJNA329194	Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of trifoliate orange (Poncirus trifoliata L. Raf.)	24.44 Gb	not applicable	not applicable	not applicable
PRJNA314020	Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research	0.89 Mb	not applicable	not applicable	not applicable
PRJNA279929	Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress	3.93 Gb	not applicable	not applicable	not applicable