| Allium sativum | PRJEB21674 | 1KP is an international multidisciplinary consortium acquiring large-scale gene sequences for the Viridiplantae (green plants), incorporating at some phylogenetic/taxonomic level nearly all known species from angiosperms to algae. This study follows initial data releases with the remaining sequence data. | Download |
| Allium sativum | PRJNA243415 | organ-specific gene expression and metabolic pathways in fertile garlic | Download |
| Allium sativum | PRJNA273554 | Garlic (Allium sativum L.) is one of the most economically important crops, and has remarkable values in food, spice and medicine. Garlic has a large genome, and few gene sequences can be obtained from the public database. | Download |
| Allium sativum | PRJNA310793 | The aim of this study is to de novo assemble and characterize the transcriptome of garlic. | Download |
| Allium sativum | PRJNA396885 | A total of 102 garlic accession were performed for mRNA sequencing, and then were used for scoring the variations in both gene sequence (SNPs) and expression (GE) in this population. Thereafter, SNPs and GE are used for carrying out association analysis with the phenotype of shape of garlic clove, respectively, which comes to a joint decision for the candidate genes that are involved in trait. In addition, SNPs and GE data is used as genotype and phenotype, respectively, for performing eQTL analysis to ascertain the interaction among trait-controlled genes, which finally brings a regulatory network for the shape of garlic clove. Overall design: Firstly, a total of 102 garlic accession were performed for mRNA-seq by Illumina sequencing. Then, the read sequencing were aligned into the referenced transcriptome, which resulted in the identification of the variations in both gene sequence (SNPs) and expression (GE). | Download |
| Allium sativum | PRJNA472416 | Green discoloration is one of the most important problems that cause low quality of product in processing of garlic, which can be induced by low temperature stress. But the mechanism of low temperature-induced green discoloration is poorly understood. In the present study, the controlled garlic and three low temperature-treated garlic samples (stored at 4 oC with 10, 15, and 40 days, respectively) were used for genome-wide transcriptome profiling analysis. | Download |
| Allium sativum | PRJNA489986 | RNA sequencing and de novo transcriptome assembly of clove and leaf tissue samples of Snow Mountain Garlic (Allium sativum) | Download |
| Allium sativum | PRJNA522648 | The long-time asexual reproduction of garlic with garlic cloves has resulted in virus accumulation and genetic depression. The seedling propagation of garlic by means of tissue culture can both eliminate viruses and improve breeding efficiency. Aerial bulbs are the first-choice materials for virus-free seed-breading of garlic under external condition, but aerial bulbs are featured by dormancy just like garlic bulbs, and low temperature or GA3 can quickly break dormancy. This research is designed to use high-throughput sequencing method to perform the sequencing research of dormant aerial bulbs and those dormancy breaking; to screen out the key differential expression genes of aerial bulbs corresponding to low temperature or GA3; and to provide a theoretical basis for exploring the molecular mechanism for dormancy breaking of aerial bulbs. | Download |
| Allium sativum | PRJNA526984 | Transcriptome sequencing was used to study dormant and GA3-treated aerial bulbs. Differentially expressed genes in the aerial bulbs after GA3 treatment were analyzed and screened, and the relationship between the differentially expressed genes and GA3 breaking dormancy of aerial bulbs was explored. | Download |
| Allium sativum | PRJNA542224 | The long-followed practice of using garlic cloves for garlic asexual reproduction has resulted in virus accumulation and genetic depression. Aerial bulbs, the preferred material for virus-free garlic seedling cultivation in vitro, undergo dormancy, but gibberellin can quickly break this state. In this study, exogenous GA3 was applied to dormant aerial bulbs, and transcriptome sequencing was then performed using dormant and gibberellin-treated aerial bulbs. Genes differentially expressed in response to the gibberellin treatment were analyzed and screened, and their relationship to GA3-induced dormancy break of aerial bulbs was explored. | Download |
| Allium sativum | PRJNA565115 | RNA-seq data of 1-cm-thick stem piece of garlic on the second day after water treatment or gibberellins treatment | Download |
| Allium sativum | PRJNA566287 | Cross-path in the dark: garlic vernalization orchestrates meristem transition via circadian rhythm and photoperiodic pathway | Download |
| Allium sativum | PRJNA607255 | To characterize the expression of 58219 genes annotated from garlic genome, the transcriptomes of seven tissues (including garlic sprouts, shoots, bulbs, flowers, roots, pesudostems, and leaves) were sequenced, and finally identified 45,750 genes expressed in various tissues investigated. In addition, the bulbs-transcriptomes in the eight stages of bulbs-development were sequenced, resulting in 6,234 genes isentified to show dynamic expression changes in the bulbs-developmental process. Overall design: The garlic Ershuizao cultivated in the experimental farm of the Shandong Agricultural University, Taian, China, in Oct. 2018 was used for the transcriptome analysis. When the garlic buds, the shoots were collected. In May 2019, the leaves, bulbs, pesudostems, garlic sprouts, roots and flowers were individually sampled. In addition, to characterize the expression of expanding bulbs dynamically, bulbs samples from eight stages of growth were collected, by sample each five day from April 11 to May 16 in 2019 when the bulbs have not start the expanding growth and have finished the expansion, respectively, and correspondingly, the sample names were designated orderly from S1 to S8. Three replicates were performed for each sample. Total RNAs for all 42 samples were separately extracted and used to construct the cDNA library with fragment lengths of ~250 bp. Thereafter, paired-end sequencing was performed for these 48 samples using the Illumina HiSeq 2500 sequencing platform | Download |
| Allium sativum | PRJNA647152 | From embryo to adult: low temperatures affect phase transitions of Allium sativum from the germination to flowering | Download |
| Allium sativum | PRJNA650017 | De Novo Assembly and Characterization of Transcriptome of Garlic clove and leaf(Allium sativum) using Illumina Paired-End Sequencing | Download |
| Allium sativum | PRJNA665946 | Transcriptome sequencing analysis was done to evaluate the transcriptional response to long day and short day in Allium sativum. | Download |
| Allium sativum | PRJNA682570 | The transcriptomes of leaves and roots between salt-tolerant and salt-sensitive garlic accessions were compared to investigate the molecular mechanisms in garlic in response to salinity. | Download |
| Allium sativum | PRJNA683607 | Garlic in the bolting/bulbing stage is most sensitive to drought stress. Therefore, an examination of molecular responses of garlic to drought stress in this stage will likely identify the drought tolerance mechanism in garlic. In this study, bolting/bulbing garlic hardneck cultivar (Purple Glazer) were exposed to drought stress for seven days. Transcriptomic analysis of garlic leaves under normal conditions and drought stress to identify candidate genes that regulate drought tolerance in garlic. | Download |
| Allium sativum | PRJNA733307 | Garlic is an important vegetable crop, widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, a comprehensive full-length transcript sets were constructed. We detected the difference in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic and protected from light at the same time. The results showed that 60087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, EGGNOG and Swiss Prot databases, and a total of 30082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes, of which 529 genes were up-regulated and 394 genes were down-regulated. Through KEGG and GO enrichment analysis, it is found that the most significant way of enriching differentially expressed genes is the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins, 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. We selected 10 candidate genes in the phenylpropane pathway for qRT-PCR quantitative verification, which verified the reliability of the RNA-Seq data. This study explored the mechanism of changes at the molecular level of garlic greening and found that the phenylpropanoid metabolic pathway has an important influence on the formation of garlic chlorophyll. This work provides a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industry | Download |
| Allium sativum | PRJNA771547 | To explore the influence of virus-accumulation on garlic growth, we produced a virus-free garlic using the landrace “Chalingzipisuan†with great accumulation of viruses, based on the shoot-tip culture. Then, using the viruses-accumulated garlic and corresponding virus-free garlic, we performed a transcriptomic investigation for the enlarging-growth bulbs, and identified 1,182 garlic genes with differential expression, suggesting these genes involved in the response to viruses-infection Overall design: The viruses-accumulated garlic was used as the treatment, and virus-free garlic was used as the control. Three biological replicates were performed for each sample. The garlic were infected by four viruses, namely, garlic virus A, D, and X, and garlic latent virus | Download |
| Allium sativum | PRJNA771548 | The garlic landrace of ‘Chalingzipisuan’ was used for transcriptome analysis. The axillary bud of garlic is at the base of clove, whereas the storage leaf at the upper clove provides essential nutrition for the germination and seedling growth. Therefore, the basal and storage clove were ere separately performed for RNA sequencing from the bulbs under three different developmental stages (i.e., enlarging growth, dormancy, and germination), generating in total 77-85 million reads. Overall design: The basal and storage clove collected from three developmental stages were separately performed for RNA sequencing. Three biological replicates of each treatment were used. Therefore, a total of 18 samples were performed for RNA sequencing. | Download |
| Allium sativum | PRJNA772184 | A total of 84 diverse germplasms collected from 13 countries were performed for population transcriptomic analysis. Then, Pearson’s correlation analysis was performed between four bulb traits and FPKM values of each gene in 84 accession, thereby to identify genes with an expressed association with bulb traits. Overall design: Three enlarging-growth bulbs of each accessions were collected and performed for RNA sequencing. | Download |
| Allium sativum | PRJNA778905 | Studying the dormancy release mechanism of garlic can sow in advance or prolong the storage period of garlic in production, which has great theoretical significance and practical value for improving the production efficiency and storage quality of garlic. | Download |
| Allium sativum | PRJNA870502 | To explore the clove enlarging growth-related genes, we compared the transcriptome of bulbs whose cloves are before enlargement and under enlarging-growth, respectively, using three garlic accessions, Chalingzipisuan, Ershuizao, and Yuanjiangyangsuan. Consequently, 4,658 genes were identified with a differential expression in at least two of three examined accessions. Overall design: For each accession, bulbs of five plants were pooled as a sample. In addition, three varieties, Chalingzipisuan, Ershuizao, and Yuanjiangyangsuan, were planted in the farm of Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, China, in Oct. of 2019; and in the Feb. and Mar. of 2020, when the bulbs had not initiated to enlarge and were under enlarging growth, respectively, the parts of bulbs were collected. Three individuals were used as three replications | Download |
| Allium cepa | PRJDB3595 | Our research via the usage of a complete set of Allium fistulosum - A. cepa monosomic addition lines aims to enable a holistic approach to profile the phytochemical composition as well as its related gene expression of Allium vegetables for plant breeding studies, through collaborative development of resources for metabolomics-high throughput chemical profiling by mass spectrometry, together with transcriptmics assay metadata by RNA-Seq. An omics approach will be used to characterize variation in these unique genetic stocks, developing capability and plant materials to support metabolomics-informed plant breeding studies of whole plants, as well as enabling detection of associations between phytochemical content, gene expression and specific genome regions. The knowledge and technologies will be applicable for targeting breeding towards enhanced functionality as well as disease resistance. | Download |
| Allium cepa | PRJNA246669 | Raw reads from two Allium cepa cultivars, H6 and SP3B | Download |
| Allium cepa | PRJNA248253 | Allium cepa is one of the highly consumed vegetable on globe which is well known for its flavor, nutritional and medicinal values. It contains phenolics and flavonoids that have potential anti-inflammatory, anti-cholesterol, anti-cancer and anti-oxidant properties. Despite many health benefits, onions cause allergies for considerable number of people. In this context, we have sequenced and anlaysed onion bulb trascripts to screen for their food allergens and cross reactive proteins which will be useful in diagnosis and targetted therapy. | Download |
| Allium cepa | PRJNA268891 | To isolate candidate genes responsible for bulb color difference in onions | Download |
| Allium cepa | PRJNA280142 | For identification of candidate genes for restorer-of-fertility gene in onion | Download |
| Allium cepa | PRJNA292137 | Transcriptome analysis of Doubled Haploid reference onion genotype 'CUDH2107' developed at Cornell University | Download |
| Allium cepa | PRJNA298934 | Bulb onion (A.cepa) two lines were selected cold and freezing susceptible and tolerance, treated with stress | Download |
| Allium cepa | PRJNA310814 | The aim of this study is to de novo assemble and characterize the transcriptome of onion | Download |
| Allium cepa | PRJNA310820 | The aim of this study is to de novo assemble and characterize the transcriptome of A. cepa var.agrogarum | Download |
| Allium cepa | PRJNA338256 | Development of onion lines with robust resistance to Fusarium basal rot requires understanding of the interaction between the pathogens and their hosts. Fusarium spp. isolates ex. onion were sequenced with an aim to assemble lineage specific region in the F. oxysporum f. sp. cepae genome and identify putative effectors modulating host resistance. Inclusion of non-pathogenic isolates and closely related species aids identification of these lineage specific regions. | Download |
| Allium cepa | PRJNA420926 | Purple blotch (PB) caused by Alternaria porri is a major disease in all onion growing countries of the world. In India, it is particularly devastating causing yield losses that range from 2.5% to 90%. The molecular mechanism underlying the interaction between the host and the pathogen is still unclear. Here we present the dynamic transcriptome profiling of Allium cepa post infection with Alternaria porri to understand the mechanism of resistance response. | Download |
| Allium cepa | PRJNA542932 | This project represents a selection of land plants in which the telomerase RNA subunit was either identified or predicted in the transcriptomic NGS data. The total RNA was extracted by TRI-REAGENT (MRC). Ribosomal RNA was depleted using Ribo-Zero (Plant) kit (Illumina). RNAseq libraries were prepared using NEBNEXT Ultra II RNA Directional Kit (NEB). Raw reads were assembled in TRINITY. | Download |
| Allium cepa | PRJNA595061 | Onion (Allium cepa L.) is one of the most important vegetable crops. It is a shallow rooted plant and thus prone to the drought stress. Therefore information generated from trasncriptome analyses will help in better understanding of molecular mechanisms behind drought response in onion | Download |
| Allium cepa | PRJNA60277 | transcriptome traces and assemblies from 2 onion genotypes from Plant and Food Research center, New Zealand | Download |
| Allium cepa | PRJNA636125 | Onion de-novo transcriptome assembly, functional annotation and RNA-Seq for Ethylene treatment to prolong dormancy | Download |
| Allium cepa | PRJNA705049 | In addition to the previously reported restorer-of-fertility (Rf) locus, Ms, a novel Rf locus was identified in this study from onion populations in which the Ms locus was fixed as a homozygous recessive genotype. A combined approach of bulked segregant analysis and RNA-seq was used to identify a chromosomal location of the novel Rf locus and to develop tightly linked molecular markers. | Download |
| Allium cepa | PRJNA796147 | Purple blotch (PB) is one of the most destructive foliar diseases of onion and other alliums, caused by a necrotrophic fungal pathogen Alternaria porri. There are no reports on the molecular response of onion to purple blotch infection. In order to elucidate the response of onion to A. porri infection. This is the first report of transcriptome profiling in onion in response to PB infection and will serve as a resource for future studies to elucidate the molecular mechanism of onion-A. porri interaction and to improve PB resistance in onions. | Download |
| Allium cepa | PRJNA803261 | The exploring genes related to gray mold resistance in onion and their application to breeding of resistant onion lines will support effective and ecological control methods of the disease. In vitro gray mold infection was conducted with a resistant and a susceptible onion line, and inoculated leaf samples were collected for obtaining transcript sequences in time series. | Download |
| Allium cepa | PRJNA881768 | RNA sequencing of Allium cepa | Download |
| Allium fistulosum | CNP0002276 | Assemblies,annotation,assemble and resequence raw data of bunching onion genome | Download |
| Allium fistulosum | PRJDB3595 | Our research via the usage of a complete set of Allium fistulosum - A. cepa monosomic addition lines aims to enable a holistic approach to profile the phytochemical composition as well as its related gene expression of Allium vegetables for plant breeding studies, through collaborative development of resources for metabolomics-high throughput chemical profiling by mass spectrometry, together with transcriptmics assay metadata by RNA-Seq. An omics approach will be used to characterize variation in these unique genetic stocks, developing capability and plant materials to support metabolomics-informed plant breeding studies of whole plants, as well as enabling detection of associations between phytochemical content, gene expression and specific genome regions. The knowledge and technologies will be applicable for targeting breeding towards enhanced functionality as well as disease resistance. | Download |
| Allium fistulosum | PRJDB863 | Transcriptome sequencing to produce an EST-based genetic map of bunching onion | Download |
| Allium fistulosum | PRJNA261868 | the goal of this project is to explore waxy related genes and pathways in Welsh onion | Download |
| Allium fistulosum | PRJNA310821 | The aim of this study is to de novo assemble and characterize the transcriptome of welsh onion | Download |
| Allium fistulosum | PRJNA504406 | We investigated transcriptomics analysis of welsh onion in response to altered nitrogen supply. Approximately 800 genes were significantly differentially regulated with different N-fertilizers. | Download |
| Allium fistulosum | PRJNA542932 | This project represents a selection of land plants in which the telomerase RNA subunit was either identified or predicted in the transcriptomic NGS data. The total RNA was extracted by TRI-REAGENT (MRC). Ribosomal RNA was depleted using Ribo-Zero (Plant) kit (Illumina). RNAseq libraries were prepared using NEBNEXT Ultra II RNA Directional Kit (NEB). Raw reads were assembled in TRINITY. | Download |
| Allium fistulosum | PRJNA827977 | Study on the metabolism of anthocyanins and flavonoids in Allium.fistulosum | Download |