These datasets hold great promise to help understand how plant biology reacts to this unique … Therefore, based on the Shiny and bootstrap frameworks, we developed the Plant Single Cell Transcriptome Hub (PsctH) ( http://jinlab.hzau.edu.cn/PsctH/ ), aiming to provide a comprehensive and accurate resource of cell markers and web tool for various cell types in tissues of plant species (Figure 1a ). Plants may enter into a state of alert that allows them to deploy defensive measures in a more effective way upon stress occurrence. Based on the transcriptome sequence data of T. rupestris, 30 single nucleotide polymorphisms (SNP) were developed and characterized in 46 individuals from two populations using high resolution … Plant TranscriptionFactor Database. Taihangia rupestris is an endangered plant species, which is disjunctively and sporadically distributed on cliff faces in the southern part of Taihang Moutains, China. Nucleic Acids Research, 36: D966-D969. Despite notable advances in the assembly of short reads, the clustering of transcripts into unigene-like (locus-specific) clusters remains a somewhat neglected subject. Access is freely given but if you publish using the data we would appreciate that you cite the following manuscripts. We first sequenced approximately 40,000 sorghum FL-cDNA reads. T. urartu: 86,247, T. turgidum: 140,118. The R. cantleyi flower transcriptome assembly was deposited in the TSA database with the accession number GIQT00000000. PlantTFDB - Plant Transcription Factor Database @ CBI, PKU. Open reading frames ORFs start at ATG and end at the stop codon unless they are truncated. De novo transcriptome characterization from Next Generation Sequencing data has become an important approach in the study of non-model plants. To identify the viruses in tree peony plants associated with the symptoms of yellowing, leaf rolling, stunted growth, and decline, high-throughput sequencing of small RNA and mRNA was conducted from a single symptomatic plant. 3. For species without genome information, transcriptome sequencing can effectively characterize and identify the biosynthesis pathway of secondary metabolites in plants, reveal the growth, development, physiological adaptability of plants, and explore the gene sequence and expression level [22–24]. Furthermore, we will incorporate additional bioinformatics tools for easier data access and online analyses. 108 , 1815-1829 [Research article] ... Open access publications in the SLU publication database is powored by EPrints 3 developed by School of Electronics and Computer Science … In the present study, transcriptome and metabolome analyses were … EST-SSR markers were developed from Pongamia pinnata transcriptome libraries. (e) Tissue expression viewer. The websites of Gao Lab have migrated into the cloud. This database covers a multitude of genome-wide transcriptome profiles of M. truncatula, being derived from two different platforms. Three biological replicates were adopted at each time … G Model CRASS3-3347; No. Of the 12,963 unigenes, 285 were annotated to the terpenoid pathways using the PlantCyc database. (a) Summary of statistics for transcriptome sequencing of diverse tissue types of B. napus. Users can find the new url below. StGDB, a new genome database for the potato (Solanum tuberosum) … The omics studies of model plants inspire us from the perspective of comparative analysis. ExPath , is also a plant transcriptomics database, which collects more than 1000 samples in biotic stress, abiotic stress, and hormone secretion. ‘WGH Dwarf’ (referred to as W2) is a stable dwarf mutant of wild-type Williams banana ‘WGH’ (Musa spp. The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Excised leaves were treated with nitrate in vitro to ensure that the measured N-response was only to locally supplied N, uninfluenced by … AAA group, referred to as H1) and ‘Nalong … Leaf color variation is a common trait in plants and widely distributed in many plants. Many metabolites with pharmacological activities are present in the tissues of P. taeda. Objectives Phytohormones are small signaling molecules with crucial roles in plant growth, development, and environmental adaptation to biotic and abiotic stress responses. Whole transcriptome research provides a fast, high-throughput means to obtain plant gene function data as well as insight into the biosynthesis of active ingredients and their regulation . Over 155 million 100-bp paired-end reads were assembled into a transcriptome database of 360,689 contigs, of which 18,660 contigs were differentially expressed between leaves and flowers. Genomics Database chevron_right; ... Retroelements, the prevalent class of plant transposons, have major impacts on host genome integrity and evolution. PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. First, in a noble gesture honoring pre-RNAseq work, publicly available GeneChip-based expression profiles have now earned a new life in the form of the legacy ‘The Medicago truncatula Gene Expression Atlas (MtGEA) Project’. of Pages 13 C. R. Biologies xxx (2015) xxx–xxx Contents lists available at ScienceDirect Comptes Rendus Biologies www.sciencedirect.com Molecular biology and genetics/Biologie et génétique moléculaires RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress Ahmed Bahieldin a,*,b, Ahmed Atef a, Jamal … Why Transcriptome Project? This transcriptome data has been used to study nodule and seed development in M. truncatula (Benedito et al., 2008). AAA group) (referred to as H2).In addition, the comparison between ‘Tianbao’ banana (Musa spp. The realDB Version 1.0 database is the first release and will be updated when new datasets are available. Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu XC, He K, Luo JC. https://www.frontiersin.org/articles/10.3389/fpls.2021.729161 The ab inito transcriptome assembly for each plant species was performed with Cufflinks v2.2.1 to generate a comprehensive catalog of novel lncRNA transcripts. Therefore,basedontheShiny andbootstrap frameworks, Therefore, transcriptome technology was widely used as an effective means to research the biosynthesis of active compounds and the mining of key enzyme genes. A transcriptome is a whole set of transcribed RNAs from a specific tissue or cell type at a developmental stage or under certain conditions . Function annotation of full-length A. mongholicus transcriptome. Genome-wide transcriptome analysis provides systems-level insights into plant biology. Data visualization is one of the first steps in assessment and … Functional annotation of R. cantleyi transcriptome PlantRegMap/PlantTFDB v5.0. The scientific database is based on the data of CNGBdb to construct multiple databases of multi-omics,aiming to provide scientific data services for different research areas, such as plant, animal, micro organism, virus, disease and health, etc., support the needs of researchers, enhance the value of data. Plant Materials and Cultivation Conditions. Additionally, 14 terpene synthase genes were identified from the transcriptome. ! AprGPD is composed of six modules, including genome, predicted genes and proteins, functional annotations and gene expression profiles. Access to RNA-sequencing data from 1173 plant species: The 1000 plant transcriptomes initiative (1KP). GigaScience 8: giz126. PMID: 31644802. DOI: 10.1093/gigascience/giz126 In this work, four banana resources were selected for experimentation. These data are housed in an open-access web-based database, TraVA ( T ranscriptome V ariation A nalysis, http://travadb.org/ ), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages. The expression patterns of the 16 genes related to terpenoid biosynthesis were analyzed by RT-qPCR to explore their putative functions. Epub 2018 Sep 26. … The remaining high-quality reads were named clean reads and mapped to GenBank, the Rfam database 76 and the transcriptome for sRNA annotation. Nitrate-responsive leaf transcriptome of japonica rice. D008: Transcriptome or gene expression of various fruit tissue in FW3.2 NILs; D009: Tissue-specific transcriptome profiling of Solanum pimpinellifolium ovaries and fruit using LCM-coupled to RNA-seq; D010: Transcriptome sequencing of leaves of resistant (RG-PtoR) and susceptible (RG-prf3 and RG-prf19) tomato plants treated with Pst DC3000 PPDB is a Plant Proteome DataBase for Arabidopsis thaliana and maize (Zea mays). An atlas of the Norway spruce needle seasonal transcriptome. In this study, a leaf color mutation in Camellia japonica (cultivar named as Maguxianzi, M) was used as material, and the mechanism of leaf color variation was revealed by physiological, cytological, transcriptome and microbiome analyses. Transcriptome analysis revealed seven differentially expressed genes related to amino acid synthesis and transporter, three of which were up-regulated and four were down-regulated. The Rice Expression Profile Database (RiceXPro) is a repository of gene expression profiles derived from microarray analysis of tissues/organs encompassing the entire growth of the rice plant under natural field conditions, rice seedlings treated with various phytohormones, and specific cell types/tissues isolated by laser microdissection (LMD). pinnata is a non-edible oil, seed-bearing leguminous tree well known for its multipurpose benefits and acts as a potential source for … An open-source database for comparative and functional genomics in forest trees and woody plant species. Available data include genomes, gene models, transcriptomes, gene expression, functional annotation, and genetic markers. • The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. his transcriptome data has been used to study nodule and seed development in M. truncatula (Benedito et al., 2008). Access is freely given but if you publish using the data we would appreciate that you cite the following manuscripts. A full-length transcriptome database was established, after which the expression patterns of some dormancy-related DEGs at the Corm, Str_S, and other stages were analyzed. In order to ascertain strategies of medicinal plants in adapting to environmental stresses and for the sake of guiding protection and ecological planting, the baseline data of the Dichocarpum transcriptome and metabolome are indispensable. In addition, transcriptome data from plants subjected to various abiotic and biotic stresses and data from speciic cell and tissue types are also included in MtGEA. As described above, we collected time-course rice transcriptome data under various types of abiotic stresses and plant hormone treatments using mRNA-Seq. UniVIO: a multiple omics database with hormonome and transcriptome data from rice. These tissue-specific gene expression data, which are mapped to the mouse genome, are available in a searchable format in the Mouse Reference Transcriptome Database. In this database, users can access predominantly two types of transcriptome data; correct TSSs and structural gene annotation based on approximately 40,000 FL-cDNAs, and expression profiles from RNA-Seq analysis. Plant Single Cell Transcriptome Hub (PsctH): an integrated online tool to explore the plant single-cell transcriptome landscape ... database and exploit efficient tools to analyze such scattered over thousands marker genes of specific cell types from different plant species. The results of this study have helped to further characterize the P. sibiricum seed dormancy trait and may form the basis of future related investigations. (b) The homepage of BnTIR. To provide valuable resources and tools for rice transcriptome analysis, we developed a database named ‘Transcriptome ENcyclopedia Of Rice (TENOR)’. However, the biosynthesis regulatory mechanisms of these metabolites are poorly understood. Results: We have constructed a comprehensive database, the plant stress RNA-Seq nexus (PSRN), which includes 12 plant species, 26 plant-stress RNA-Seq datasets, and 937 samples. The ab inito transcriptome assembly for each plant species was performed with Cufflinks v2.2.1 to generate a comprehensive catalog of novel lncRNA transcripts. Despite several previously published molecular studies focused on plant hormones, our understanding of the transcriptome induced by phytohormones remains unclear, especially in … BnTIR is a refined transcriptome platform for Brassica napus. been fundamental to study gene expression in many plants; however, this technology is biased toward known RNAs used to generate the probes in the chips. Published transcriptome information was mainly derived from roots, stems, and leaves of the plant, with little transcriptome information for … Recent advances in the routine access to space along with increasing opportunities to perform plant growth experiments on board the International Space Station have led to an ever-increasing body of transcriptomic, proteomic, and epigenomic data from plants experiencing spaceflight. (d) eFP viewer. To get cognate transcription factor information of Nakai, all unigenes were examined from the plant TFDB database by the HMMER analysis method. Transcriptome sequencing, de novo assembly, functional annotation and classification. InterPro analysis shows that 30,403 sequences have been functionally characterized against its member database. (2008). TSA is an archive of computationally assembled transcript sequences from primary data such as ESTs and Next Generation Sequencing Technologies. Specifically, amino acid transporter YPQ gene was down-regulated 2.93-fold (Table S6). To build STAR aligner indexes, the corresponding reference genome assemblies in multi-FASTA format were downloaded from the ftp site of Ensembl Plants database release 31 . The TraVA database can be accessed at http://travadb.org/browse/Species=Phalaenopsis_equestris/. It also provides diverse analyses including co-expression analysis, DEG identification, and enrichment analysis of pathways. The plant Reactome is a database of plant metabolic and regulatory pathways which have been curated for the reference species rice and applied to 58 other plant species . ... Table S8: The number of downregulated genes grouped in each pathway by Plant Reactome database. To get cognate transcription factor information of Nakai, all unigenes were examined from the plant TFDB database by the HMMER analysis method. 2018 Aug;16 (4):283-293. doi: 10.1016/j.gpb.2018.08.002. Genomics Proteomics Bioinformatics. In recent years, de novo transcriptome sequencing is applied to multiple medicinal plants to reveal the genetic information and regulatory mechanisms of specific metabolite production in diverse medicinal plants. series for nodules and seeds. Initially PPDB was dedicated to plant plastids, but has now expanded to the whole plant proteome – hence it was renamed from Plastid PDB to Plant PDB in November 2007. RNA-seq technology is an effective method to introduce transcriptome database, which can provide large numbers of coding sequences (CDS) with non-coding and repetitive sequences excluded. PSRN is an open resource for intuitive data exploration, providing expression profiles of coding-transcript/lncRNA and identifying which transcripts are differentially expressed between different stress-specific subsets, in order to support researchers generating new biological insights and hypotheses in molecular breeding or evolution. This database is part of a … Due to the limited depth of quantitative proteomics our understanding of gene–protein–complex stoichiometry is largely unknown in plants. Bioinformatic analyses and reconstruction of viral genomes indicated mixed viral infections involving cycas necrotic stunt … The bacterium was initially isolated from the rhizosphere of sugarcane. Transcriptome profiling in conifers and the PiceaGenExpress database show patterns of diversification within gene families and interspecific conservation in vascular gene expression Conifers have very large genomes (13 to 30 Gigabases) that are mostly uncharacterized although extensive cDNA resources have recently become available. (c) Architecture of BnTIR database, including data source layer, middleware layer, and application layer. 3.2. Hardwood Genomics Project. protein-coding transcriptome were collected from Phy-tozome v11 [23], Ensembl Plants [24], and PopGenIE [25]. In addition to transcriptome annotations collected from the abovementioned databases, the transcriptome of each species was employed for homology searches against plant sequences retrieved from the NCBI RefSeq database using the NCBI BLAST+ toolkit , version 2.3.0, with an E-value threshold of 1E-3. ONEKP: BLAST for 1,000 Plants This website performs BLAST searches on the 1000 plant (1KP) trancriptomes data described in the following publications. PlantTFDB: a comprehensive plant transcription factor database. The transcriptome of R. palmatum was assembled with the RNA-seq method and 140,224 unigenes were screened out in our previous study. In addition, transcriptome data from plants subjected to various abiotic and biotic stresses and data from specific cell and tissue types are also included in MtGEA. Plants have been and continue to be a source of medicinal compounds. Plant Journal. To build STAR aligner indexes, the corresponding reference genome assemblies in multi-FASTA format were downloaded from the ftp site of Ensembl Plants database release 31 . Methods Mol Biol., 674:351-68. Furthermore, absence of a specific annotated gene in a plant genome/transcriptome does not necessarily mean that the plant cannot perform a particular function. Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth.In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water … To explore the gene expression mode responding to the dynamics of phytohormones during the developmental process of the L. cubeba pericarp, RNA-seq was employed to exhibit the transcriptional gene expression profile. High-quality genomic DNA was extracted from fresh leaves using … The Mouse Transcriptome Project was an NIH-supported initiative that generated a free, public database of gene transcripts for many mouse tissues. Initially PPDB was dedicated to plant plastids, but has now expanded to the whole plant proteome – hence it was renamed from Plastid PDB to Plant PDB in November 2007. To determine seed-specificity for each set of genes, transcript data from the two transcriptomic databases were grouped into two categories: developing seeds and other tissues. Results -Tissue-specific expression of SEEDgenes Recently, Lotus Computational identification of plant transcription factors and the construction of the PlantTFDB database. UniVIO: a multiple omics database with hormonome and transcriptome data from rice. Plant Cell Physiol (2013) by T Kudo, K Akiyama, M Kojima, N Makita, T Sakurai, H Sakakibara Indeed, closely related paralogous transcripts … The College of Pharmacy of the University of Illinois at Chicago (UIC) and its medicinal plant resource, the Dorothy Bradley Atkins Medicinal Plants Garden , is a member of a consortium to study and to understand the complete formation, storage and regulation of plant-derived medicinal compounds at the enzyme and gene level ("Transcriptome characterization … Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. 1000 Plant (1KP) Transcriptomes is a large-scale international multidisciplinary consortium acquiring data from over 1,000 plant species (from angiosperms to algae) based on the next generation sequencing technology. In this study, the database of apricot genome and phenotype was established, which provides a database of comprehensive phenotype, genome, and transcriptome resources of apricots. Genome-wide transcription studies improve our understanding of gene function and the complex mechanisms involved in regulating gene expression. This integrative transcriptome could serve as an alternative genomic reference for the molecular exploration of Bougainvillea and will … Application of transcriptomics in plant breeding • 2- Small RNA characterization: Small RNAs (sRNA) are non-protein-coding small RNA molecules ranging from 20 to 30 nt that have a role in development, genome maintenance and plant responses to environmental stresses. D008: Transcriptome or gene expression of various fruit tissue in FW3.2 NILs; D009: Tissue-specific transcriptome profiling of Solanum pimpinellifolium ovaries and fruit using LCM-coupled to RNA-seq; D010: Transcriptome sequencing of leaves of resistant (RG-PtoR) and susceptible (RG-prf3 and RG-prf19) tomato plants treated with Pst DC3000 Plant Cell Physiol (2013) by T Kudo, K Akiyama, M Kojima, N Makita, T Sakurai, H Sakakibara We have generated three transcriptome datasets, for Triticum urartu, Triticum turgidum and a complementary set of published wheat transcripts not present in the T. turgidum set.. The diazotrophic Burkholderia anthina MYSP113 is a vital plant growth-promoting bacteria and sugarcane root association. Here, cDNA libraries of O. dubium leaves and flowers were constructed and sequenced using the Illumina HiSeq 2500. We only Transcripts Datasets include 5' and 3' untranslated regions. This phenomenon is termed defense priming, and it is started in plants with a still enigmatic priming phase in which complex molecular and physiological changes occur. All samples are assigned to 133 stress-specific subsets, which are constructed into 254 subset pairs, a comparison between selected two subsets, for stress-specific differentially expressed … Table S9: RNA integrity number (RIN) scores of twelve RNA samples in transcriptome analysis experiments. Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely been examined below the species level. Loblolly pine (Pinus taeda L.) is an important tree for afforestation with substantial economic and ecological value. Plant hormones play important roles in inducing anthocyanin accumulation. Analysis of their completeness using plant BUSCOs found that the completeness of these two transcripts datasets of tea plant generated using third-generation sequencing varied significantly, ranging from 55.1 to 92.7% (Additional file 1: Table S11), with the best performance showing a similar completeness of our NGS transcriptome assembly (92.5%) with 32 Gb data. We have successfully utilised EST-SSRs to study the genetic diversity of Indian P. pinnata germplasms and transferability study on legume plants.P. Of the top 150 top-selling prescribed chemical entities (drugs), circa 23% are compounds derived from plants ( Grifo et al., 1997 ). Limited depth of quantitative proteomics our understanding of gene function and the complex mechanisms involved in gene! First release and will be updated when new Datasets are available in response to the limited depth of quantitative our. Comparative and functional Genomics in forest trees and woody plant species was performed Cufflinks. 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