Anthocyanins are a major class of flavonoids that are produced in the tissues of many plant species in response to environmental signals. The pigmentation of Chinese cabbage (
Brassica rapa
) was ...analyzed using newly developed 300K
Brassica rapa
microarrays. The significantly expressed genes were analyzed by clusters of orthologous groups (COGs) and hypergeometric analyses for transcription factors associated with anthocyanin pigmentation. The candidate genes were classified into 11 groups that exhibited functionally diverse transcription factor activity involved in anthocyanin-based pigmentation. Thirty-eight unknown genes were identified that potentially play a role in anthocyanin biosynthesis. Three of these unknown genes differed dramatically among cabbage leaves with yellow, green, or red pigmentation. These three genes may play a regulatory role in the anthocyanin production process or may be related to anthocyanin metabolism during flavonoid biosynthesis. These results show functional diversity of transcription factor families and that the biological functions of the anthocyanin-related transcription factors may be activated in a pigmentation signaling pathway in Chinese cabbage (
Brassica rapa
).
Ozone (O3), a serious air pollutant, is known to significantly reduce photosynthesis, growth, and yield and to cause foliar injury and senescence. Here, integrated transcriptomics, proteomics, and ...metabolomics approaches were applied to investigate the molecular responses of O3 in the leaves of 2-week-old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O3 for a period of 24 h. On the basis of the morphological alteration of O3-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12, and 24 h using rice DNA microarray chip. A total of 1535 nonredundant genes showed altered expression of more than 5-fold over the control, representing 8 main functional categories. Genes involved in information storage and processing (10%) and cellular processing and signaling categories (24%) were highly represented within 1 h of O3 treatment; transcriptional factor and signal transduction, respectively, were the main subcategories. Genes categorized into information storage and processing (17, 23%), cellular processing and signaling (20, 16%) and metabolism (18, 19%) were mainly regulated at 12 and 24 h; their main subcategories were ribosomal protein, post-translational modification, and signal transduction and secondary metabolites biosynthesis, respectively. Two-dimensional gel electrophoresis-based proteomics analyses in combination with tandem mass spectrometer identified 23 differentially expressed protein spots (21 nonredundant proteins) in leaves exposed to O3 for 24 h compared to respective control. Identified proteins were found to be involved in cellular processing and signaling (32%), photosynthesis (19%), and defense (14%). Capillary electrophoresis-mass spectrometry-based metabolomic profiling revealed accumulation of amino acids, gamma-aminobutyric acid, and glutathione in O3 exposed leaves until 24 h over control. This systematic survey showed that O3 triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice.
► Genome-wide survey among six species. ► Compared potential gene birth-and-death events in the OsTRX. ► Gene duplication, evolution and synteny analysis. ► Gene expression profiles of biotic and ...abiotic stresses were observed in rice. ► Selected the candidate genes for functional analysis.
Thioredoxin (TRX) is a multi-functional redox protein. Genome-wide survey and expression profiles of different stresses were observed. Conserved amino acid residues and phylogeny construction using the OsTRX conserved domain sequence suggest that the TRX gene family can be classified broadly into six subfamilies in rice. We compared potential gene birth-and-death events in the OsTRX genes. The Ka/Ks ratio is a measure to explore the mechanism and 3 evolutionary stages of the OsTRX genes divergence after duplication. We used 270 TRX genes from monocots and eudicots for synteny analysis. Furthermore, we investigated expression profiles of this gene family under 5 biotic and 3 abiotic stresses. Several genes were differentially expressed with high levels of expression and exhibited subfunctionalization and neofunctionalization after the duplication event response to different stresses, which provides novel reference for the cloning of the most promising candidate genes from OsTRX gene family for further functional analysis.
The OsWRKY genes play various roles in developmental processes and in stress-related responses in plants. We describe the rice OsWRKY gene expression profiles (GEPs) under control, hormone-treated, ...and water-deficit treatment (WDT) conditions. The preferential expression of 3 genes was observed in specific tissues, suggesting that these genes may play important roles in the root and panicle stages of growth. To investigate the GEPs in the root and panicle of 3 rice genotypes, we used 2 near-isogenic rice lines from a common genetic combination backcross developed by Aday Selection and IR64. WDTs were applied using the fraction of transpirable soil water (FTSW) for severe, mild, and control conditions. Transcriptomic analysis using a 44K oligoarray from Affymetrix and Agilent was performed on all the tissues. The majority of the OsWRKY genes that were activated were activated in the drought-tolerant IR77298-14-1-2-B-10 line but not in the drought-susceptible IR77298-14-1-2-B-13 or IR64 lines. In IR77298-14-1-2-B-10, non-redundant genes (9) were very specific in their higher expression levels. Approximately 27 and 43% more genes from group III and subgroup IV-a, respectively, were activated in the panicle during severe stress than during the control treatment. We found 5 OsWRKY genes that introgressed in the drought-tolerant IR77298-14-1-2-B-10 line. Os01g43650 was up-regulated in the root under both WDTs and in the panicle under mild stress. OsWRKY up-regulated genes with tissue-specific expression patterns that contained at least 3 cis-elements in the tolerant line. These results provide a useful reference for the cloning of candidate genes for further functional analysis.
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the ...sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
Therefore, 3,895 candidate genes related to anthocyanin biosynthesis in Chinese cabbage were identified using a 300K
Brassica rapa
microarray analysis. Gene expression during six stages of leaf ...developmental stages were examined in FC (green leaf) and FA(red leaf) Chinese cabbage cultivars. The 317 transcription factor genes found to be associated with anthocyanin were classified into 11 functional groups. The ratio of expression levels of each transcription factor between the two cultivars was examined during the six leaf developmental stages. A total of 14 genes were found to be expressed in all developmental stages commonly. Among these genes, 10 unknown and hypothetical genes were differentially revealed to be expressed between the two cultivars at each developmental stage, as determined by microarray analysis, and were verified by RT-PCR validation. These genes most likely play regulatory roles in either anthocyanin production or metabolism during flavonoid biosynthesis. While these genes require further validation and characterization, our results illustrate the potential usefulness of this multi-layered screening method using Chinese cabbage (
Brassica rapa
) microarrays.
Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop
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(PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein–protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein–protein interactions in a wide range of organisms.
We describe a computer-based method that selects representative clones for full-length sequencing in a full-length cDNA project. Our method classifies end sequences using two kinds of criteria, ...grouping, and clustering. Grouping places together variant cDNAs, family genes, and cDNAs with sequencing errors. Clustering separates those cDNA clones into distinct clusters. The full-length sequences of the clones selected by grouping are determined preferentially, and then the sequences selected by clustering are determined. Grouping reduced the number of rice cDNA clones for full-length sequencing to 21% and mouse cDNA clones to 25%. Rice full-length sequences selected by grouping showed a 1.07-fold redundancy. Mouse full-length sequences showed a 1.04-fold redundancy, which can be reduced by approximately 30% from the selection using our previous method. To estimate the coverage of unique genes, we used FANTOM (Functional Annotation of RIKEN Mouse cDNA Clones) clusters (). Grouping covered almost all unique genes (93% of FANTOM clusters), and clustering covered all genes. Therefore, our method is useful for the selection of appropriate representative clones for full-length sequencing, thereby greatly reducing the cost, labor, and time necessary for this process.
Several genes/QTLs governing resistance/tolerance to abiotic and biotic stresses have been reported and mapped in rice. A QTL for submergence tolerance was found to be co-located with a major QTL for ...broad-spectrum bacterial leaf blight (bs-blb) resistance on the long arm of chromosome 5 in indica cultivars FR13A and IET8585. Using the Nipponbare (japonica) and 9311 (indica) genome sequences, we identified, in silico, candidate genes in the chromosomal region Kottapalli et al. (2006). Transcriptional profiling of FR13A and IET8585 using a rice 22K oligo array validated the above findings. Based on in silico analysis and arraying we observed that both cultivars respond to the above stresses through a common signaling system involving protein kinases, adenosine mono phosphate kinase, leucine rich repeat, PDZ/DHR/GLGF, and response regulator receiver protein. The combined approaches suggest that transcription factor EREBP on long arm of chromosome 5 regulates both submergence tolerance and bib resistance. Pyruvate decarboxylase and alcohol dehydrogenase, co-located in the same region, are candidate downstream genes for submergence tolerance at the seedling stage, and t-snare for bs-blb resistance. We also detected up-regulation of novel defense/stress-related genes including those encoding fumaryl aceto acetate (FAA) hydrolase, scramblase, and galactose oxidase, in response to the imposed stresses.
Expression levels of the NAC gene family were studied in rice infected with Rice dwarf virus (RDV), Rice black-streaked dwarf virus (RBSDV), Rice grassy stunt virus (RGSV), Rice ragged stunt virus ...(RRSV), and Rice transitory yellowing virus (RTYV). Microarray analysis showed that 75 (68%) OsNAC genes were differentially regulated during infection with RDV, RBSDV, RGSV, and RRSV compared with the control. The number of OsNAC genes up-regulated was highest during RGSV infection, while the lowest number was found during RTYV infection. These phenomena correlate with the severity of the syndromes induced by the virus infections. Most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated for all virus infections. These OsNAC genes might be related to the health stage maintenance of the host plants. Interestingly, most of the genes in the subgroups TIP and SNAC were more highly expressed during RBSDV and RGSV infections. These results suggested that OsNAC genes might be related to the responses induced by the virus infection. All of the genes assigned to the TIP subgroups were highly expressed during RGSV infection when compared with the control. For RDV infection, the number of activated genes was greatest during infection with the S-strain, followed by the D84-strain and the O-strain, with seven OsNAC genes up-regulated during infection by all three strains. The Os12g03050 and Os11g05614 genes showed higher expression during infection with four of the five viruses, and Os11g03310, Os11g03370, and Os07g37920 genes showed high expression during at least three viral infections. We identified some duplicate genes that are classified as neofunctional and subfunctional according to their expression levels in different viral infections. A number of putative cis-elements were identified, which may help to clarify the function of these key genes in network pathways.
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