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author:("Wang, wiping")
1.  Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes 
BMC Genomics  2015;16(1):223.
Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.
We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.
The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1442-3) contains supplementary material, which is available to authorized users.
PMCID: PMC4373064  PMID: 25888081
Grape; Chinese wild Vitis; De novo transcriptome; Disease related genes; Cis-NATs
2.  Gibberellin-induced changes in the transcriptome of grapevine (Vitis labrusca × V. vinifera) cv. Kyoho flowers 
BMC Genomics  2015;16(1):128.
Gibberellins are well known for their growth control function in flower, fruit and seed development, and as such, exogenous gibberellic acid (GA) application plays an important role in viticulture. Unfortunately, the mechanism by which GA3 acts in the regulation of these complicated developmental processes in grape remains unclear.
In the present study, we demonstrated that application of GA3 to ‘Kyoho’ grapevine inflorescences at pre-bloom promoted flower opening, and induced fruit coloring as well as seed abortion. In an attempt to obtain a deeper understanding of the molecular mechanisms driving these responses to GA3 treatment, we performed large-scale transcriptome sequencing of grape flowers following GA3 treatment using Illumina sequencing technology. Global expression profiles of GA3-treated and untreated grape flowers were compared and a large number of GA3-responsive genes were identified. Gene ontology (GO) term classification and biochemical pathway analyses indicated that GA3 treatment caused changes in the levels of transcripts involved in cellular processes, reproduction, hormone and secondary metabolism, as well as the scavenging and detoxification of reactive oxygen species (ROS). These findings suggest that GA3-induced morphological alterations may be related to the control of hormone biosynthesis and signaling, regulation of transcription factors, alteration of secondary metabolites, and the stability of redox homeostasis.
Taken together, this comprehensive inflorescence transcriptome data set provides novel insight into the response of grape flowers to GA3 treatment, and also provides possible candidate genes or markers that could be used to guide future efforts in this field.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1324-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4348105  PMID: 25888129
Grape; Gibberellic acid; Gene expression; Pathways; RNA-seq; Transcriptome
3.  Genome-Wide Identification, Evolution and Expression Analysis of the Grape (Vitis vinifera L.) Zinc Finger-Homeodomain Gene Family 
Plant zinc finger-homeodomain (ZHD) genes encode a family of transcription factors that have been demonstrated to play an important role in the regulation of plant growth and development. In this study, we identified a total of 13 ZHD genes (VvZHD) in the grape genome that were further classified into at least seven groups. Genome synteny analysis revealed that a number of VvZHD genes were present in the corresponding syntenic blocks of Arabidopsis, indicating that they arose before the divergence of these two species. Gene expression analysis showed that the identified VvZHD genes displayed distinct spatiotemporal expression patterns, and were differentially regulated under various stress conditions and hormone treatments, suggesting that the grape VvZHDs might be also involved in plant response to a variety of biotic and abiotic insults. Our work provides insightful information and knowledge about the ZHD genes in grape, which provides a framework for further characterization of their roles in regulation of stress tolerance as well as other aspects of grape productivity.
PMCID: PMC4013592  PMID: 24705465
synteny analysis; phylogenetic analysis; gene expression; grape; zinc finger-homeodomain
4.  Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family 
Journal of Experimental Botany  2014;65(6):1513-1528.
Fifty-nine VvWRKY genes were identified. Phylogenetic tree and synteny analysis revealed the specific evolutionary relationship of these genes. Meanwhile, differential expression patterns indicated their possible roles in specific tissues and under different stresses.
WRKY proteins comprise a large family of transcription factors that play important roles in plant defence regulatory networks, including responses to various biotic and abiotic stresses. To date, no large-scale study of WRKY genes has been undertaken in grape (Vitis vinifera L.). In this study, a total of 59 putative grape WRKY genes (VvWRKY) were identified and renamed on the basis of their respective chromosome distribution. A multiple sequence alignment analysis using all predicted grape WRKY genes coding sequences, together with those from Arabidopsis thaliana and tomato (Solanum lycopersicum), indicated that the 59 VvWRKY genes can be classified into three main groups (I–III). An evaluation of the duplication events suggested that several WRKY genes arose before the divergence of the grape and Arabidopsis lineages. Moreover, expression profiles derived from semiquantitative PCR and real-time quantitative PCR analyses showed distinct expression patterns in various tissues and in response to different treatments. Four VvWRKY genes showed a significantly higher expression in roots or leaves, 55 responded to varying degrees to at least one abiotic stress treatment, and the expression of 38 were altered following powdery mildew (Erysiphe necator) infection. Most VvWRKY genes were downregulated in response to abscisic acid or salicylic acid treatments, while the expression of a subset was upregulated by methyl jasmonate or ethylene treatments.
PMCID: PMC3967086  PMID: 24510937
Evolution; expression profile analysis; grape (Vitis vinifera L.); phylogenetic analysis; synteny analysis; WRKY genes.
5.  Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics 
Planta  2012;237(1):189-210.
In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD+- or NADP+-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as ‘aldehyde scavengers’ by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried outgenome-wide identification of ALDH genes in a number of plant species—including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.
PMCID: PMC3536936  PMID: 23007552
ALDH; Aldehyde dehydrogenase; Stress response; Gene family; Nomenclature
6.  Correction: Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape 
PLoS ONE  2013;8(12):10.1371/annotation/c9d9d321-b821-4060-8bf9-ff181229fea7.
PMCID: PMC3865316
7.  Genome-Wide Analysis of Respiratory Burst Oxidase Homologs in Grape (Vitis vinifera L.) 
Plant respiratory burst oxidase homolog (rboh) genes appear to play crucial roles in plant development, defense reactions and hormone signaling. In this study, a total of seven rboh genes from grape were identified and characterized. Genomic structure and predicted protein sequence analysis indicated that the sequences of plant rboh genes are highly conserved. Synteny analysis demonstrated that several Vvrboh genes were found in corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of the respective lineages. The expression pattern of Vvrboh genes in different tissues was assessed by qRT-PCR and two were constitutively expressed in all tissues tested. The expression profiles were similarly analyzed following exposure to various stresses and hormone treatments. It was shown that the expression levels of VvrbohA, VvrbohB and VvrbohC1 were significantly increased by salt and drought treatments. VvrbohB, VvrbohC2, and VvrbohD exhibited a dramatic up-regulation after powdery mildew (Uncinula necator (Schw.) Burr.) inoculation, while VvrbohH was down-regulated. Finally, salicylic acid treatment strongly stimulated the expression of VvrbohD and VvrbohH, while abscisic acid treatment induced the expression of VvrbohB and VvrbohH. These results demonstrate that the expression patterns of grape rboh genes exhibit diverse and complex stress-response expression signatures.
PMCID: PMC3876103  PMID: 24351809
reactive oxygen species; synteny analysis; phylogenetic analysis; gene expression
8.  Effect of GA3 Treatment on Seed Development and Seed-Related Gene Expression in Grape  
PLoS ONE  2013;8(11):e80044.
The phytohormone gibberellic acid (GA3) is widely used in the table grape industry to induce seedlessness in seeded varieties. However, there is a paucity of information concerning the mechanisms by which GAs induce seedlessness in grapes.
Methodology/Principal Findings
In an effort to systematically analyze the cause of this GA3-induced seed abortion, we conducted an in depth characterization of two seeded grape cultivars (‘Kyoho’ and ‘Red Globe’), along with a seedless cultivar (‘Thompson Seedless’), following treatment with GA3. In a similar fashion to the seedless control, which exhibited GA3-induced abortion of the seeds 9 days after full bloom (DAF), both ‘Kyoho’ and ‘Red Globe’ seeded varieties exhibited complete abortion of the seeds 15 DAF when treated with GA3. Morphological analyses indicated that while fertilization appeared to occur normally following GA3 treatment, as well as in the untreated seedless control cultivar, seed growth eventually ceased. In addition, we found that GA3 application had an effect on redox homeostasis, which could potentially cause cell damage and subsequent seed abortion. Furthermore, we carried out an analysis of antioxidant enzyme activities, as well as transcript levels from various genes believed to be involved in seed development, and found several differences between GA3-treated and untreated controls.
Therefore, it seems that the mechanisms driving GA3-induced seedlessness are similar in both seeded and seedless cultivars, and that the observed abortion of seeds may result at least in part from a GA3-induced increase in cell damage caused by reactive oxygen species, a decrease in antioxidant enzymatic activities, and an alteration of the expression of genes related to seed development.
PMCID: PMC3818301  PMID: 24224035
9.  Genome-wide identification, evolutionary and expression analysis of the aspartic protease gene superfamily in grape 
BMC Genomics  2013;14:554.
Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cell death, and reproduction. Prior to the present study, no grape AP gene(s) had been reported, and their research on woody species was very limited.
In this study, a total of 50 AP genes (VvAP) were identified in the grape genome, among which 30 contained the complete ASP domain. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family. Additional analysis between grape and Arabidopsis demonstrated that several grape AP genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of grape and Arabidopsis. Phylogenetic relationships of the 30 VvAPs with the complete ASP domain and their Arabidopsis orthologs, as well as their gene and protein features were analyzed and their cellular localization was predicted. Moreover, expression profiles of VvAP genes in six different tissues were determined, and their transcript abundance under various stresses and hormone treatments were measured. Twenty-seven VvAP genes were expressed in at least one of the six tissues examined; nineteen VvAPs responded to at least one abiotic stress, 12 VvAPs responded to powdery mildew infection, and most of the VvAPs responded to SA and ABA treatments. Furthermore, integrated synteny and phylogenetic analysis identified orthologous AP genes between grape and Arabidopsis, providing a unique starting point for investigating the function of grape AP genes.
The genome-wide identification, evolutionary and expression analyses of grape AP genes provide a framework for future analysis of AP genes in defining their roles during stress response. Integrated synteny and phylogenetic analyses provide novel insight into the functions of less well-studied genes using information from their better understood orthologs.
PMCID: PMC3751884  PMID: 23945092
Synteny analysis; Phylogenetic analysis; Gene expression; Orthologous genes; Grape
10.  Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids 
Genome Biology  2013;14(6):R57.
Recent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variations in hybrids given the significant heterotic performance, the well-known complexity of the genome, and the rich history in epigenetic studies. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.
Here, we generated integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes. We observed that whereas histone modifications vary both between organs and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.
These results suggest that despite variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.
PMCID: PMC3707063  PMID: 23758703
maize hybrids; transcriptome; epigenome
11.  Genomic Organization, Phylogenetic Comparison and Differential Expression of the SBP-Box Family Genes in Grape 
PLoS ONE  2013;8(3):e59358.
The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis, rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in grapevine.
Methodology/Principal Findings
Eighteen SBP-box gene family members were identified in Vitis vinifera, twelve of which bore sequences that were complementary to miRNA156/157. Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis. Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis ‘Shang-24’ revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses.
The results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop.
PMCID: PMC3601960  PMID: 23527172
12.  Genome-Wide Identification and Analysis of the TIFY Gene Family in Grape 
PLoS ONE  2012;7(9):e44465.
The TIFY gene family constitutes a plant-specific group of genes with a broad range of functions. This family encodes four subfamilies of proteins, including ZML, TIFY, PPD and JASMONATE ZIM-Domain (JAZ) proteins. JAZ proteins are targets of the SCFCOI1 complex, and function as negative regulators in the JA signaling pathway. Recently, it has been reported in both Arabidopsis and rice that TIFY genes, and especially JAZ genes, may be involved in plant defense against insect feeding, wounding, pathogens and abiotic stresses. Nonetheless, knowledge concerning the specific expression patterns and evolutionary history of plant TIFY family members is limited, especially in a woody species such as grape.
Methodology/Principal Findings
A total of two TIFY, four ZML, two PPD and 11 JAZ genes were identified in the Vitis vinifera genome. Phylogenetic analysis of TIFY protein sequences from grape, Arabidopsis and rice indicated that the grape TIFY proteins are more closely related to those of Arabidopsis than those of rice. Both segmental and tandem duplication events have been major contributors to the expansion of the grape TIFY family. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologues of several grape TIFY genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of lineages that led to grape and Arabidopsis. Analyses of microarray and quantitative real-time RT-PCR expression data revealed that grape TIFY genes are not a major player in the defense against biotrophic pathogens or viruses. However, many of these genes were responsive to JA and ABA, but not SA or ET.
The genome-wide identification, evolutionary and expression analyses of grape TIFY genes should facilitate further research of this gene family and provide new insights regarding their evolutionary history and regulatory control.
PMCID: PMC3439424  PMID: 22984514
13.  Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily 
PLoS ONE  2012;7(2):e32153.
The completion of the grape genome sequencing project has paved the way for novel gene discovery and functional analysis. Aldehyde dehydrogenases (ALDHs) comprise a gene superfamily encoding NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of endogenous and exogenous aromatic and aliphatic aldehydes. Although ALDHs have been systematically investigated in several plant species including Arabidopsis and rice, our knowledge concerning the ALDH genes, their evolutionary relationship and expression patterns in grape has been limited.
Methodology/Principal Findings
A total of 23 ALDH genes were identified in the grape genome and grouped into ten families according to the unified nomenclature system developed by the ALDH Gene Nomenclature Committee (AGNC). Members within the same grape ALDH families possess nearly identical exon-intron structures. Evolutionary analysis indicates that both segmental and tandem duplication events have contributed significantly to the expansion of grape ALDH genes. Phylogenetic analysis of ALDH protein sequences from seven plant species indicates that grape ALDHs are more closely related to those of Arabidopsis. In addition, synteny analysis between grape and Arabidopsis shows that homologs of a number of grape ALDHs are found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the speciation of the grape and Arabidopsis. Microarray gene expression analysis revealed large number of grape ALDH genes responsive to drought or salt stress. Furthermore, we found a number of ALDH genes showed significantly changed expressions in responses to infection with different pathogens and during grape berry development, suggesting novel roles of ALDH genes in plant-pathogen interactions and berry development.
The genome-wide identification, evolutionary and expression analysis of grape ALDH genes should facilitate research in this gene family and provide new insights regarding their evolution history and functional roles in plant stress tolerance.
PMCID: PMC3280228  PMID: 22355416
14.  Characterization and Expression Analysis of a Retinoblastoma-Related Gene from Chinese Wild Vitis pseudoreticulata 
Retinoblastoma-related (RBR) genes, a conserved gene family in higher eukaryotes, play important roles in cell differentiation, development, and mammalian cell death; however, little is known of their function in plants. In this study, a RBR gene was isolated from the Chinese wild grape, Vitis pseudoreticulata W. T. Wang clone “Baihe-35-1”, and designated as VpRBR. The cDNA sequence of VpRBR was 3,030 bp and contained an open reading frame of 3,024 bp. Conceptual translation of this gene indicated a composition of 1,007 amino acids with a predicted molecular mass of 117.3 kDa. The predicted protein showed a retinoblastoma-associated protein domain A from amino acid residues 416 to 579, and domain B from residues 726 to 855. The result of expression analysis indicated that VpRBR was expressed in tissues, leaves, stem, tendrils, flower, and grape skin at different expression levels. Further quantitative reverse transcription-PCR (qRT-PCR) data indicated that VpRBR levels were higher in Erysiphe necator-treated “Baihe-35-1” and “Baihe-13-1”, two resistant clones of Chinese wild V. pseudoreticulata, than in E. necator-treated “Hunan-1”, a susceptible clone of V. pseudoreticulata. Furthermore, the expression of VpRBR in response to salicylic acid (SA), methyl jasmonate (MeJA), and ethylene (Eth) in grape leaves was also investigated. Taken together, these data indicate that VpRBR may contribute to some aspect of powdery mildew resistance in grape.
PMCID: PMC3881572  PMID: 24415838
Vitis pseudoreticulata; Retinoblastoma-related gene; Powdery mildew; Expression analysis
15.  Characterization of Erysiphe necator-Responsive Genes in Chinese Wild Vitis quinquangularis 
Powdery mildew (PM), caused by fungus Erysiphe necator, is one of the most devastating diseases of grapevine. To better understand grapevine-PM interaction and provide candidate resources for grapevine breeding, a suppression subtractive hybridization (SSH) cDNA library was constructed from E. necator-infected leaves of a resistant Chinese wild Vitis quinquangularis clone “Shang-24”. A total of 492 high quality expressed sequence tags (ESTs) were obtained and assembled into 266 unigenes. Gene ontology (GO) analysis indicated that 188 unigenes could be assigned with at least one GO term in the biological process category, and 176 in the molecular function category. Sequence analysis showed that a large number of these genes were homologous to those involved in defense responses. Genes involved in metabolism, photosynthesis, transport and signal transduction were also enriched in the library. Expression analysis of 13 selected genes by qRT-PCR revealed that most were induced more quickly and intensely in the resistant material “Shang-24” than in the sensitive V. pseudoreticulata clone “Hunan-1” by E. necator infection. The ESTs reported here provide new clues to understand the disease-resistance mechanism in Chinese wild grapevine species and may enable us to investigate E. necator-responsive genes involved in PM resistance in grapevine germplasm.
PMCID: PMC3472759  PMID: 23109867
Chinese wild Vitis quinquangularis; Erysiphe necator; SSH; EST; qRT-PCR
16.  Ethephon Promotes Germination of Echinacea angustifolia and E. pallida in Darkness 
Seeds from five lots each of Echinacea angustifolia DC, and E. pallida (Nutt.) Nutt. were germinated in a growth chamber in light (40 μmol·m−2· s−1) or darkness at 25 °C for 16 to 20 d after soaking in 1 mM ethephon or water for 10 min, or moist stratification at 4 – 6 °C for two weeks. Either light or ethephon promoted seed germination of E. angustifolia and E. pallida, in comparison with darkness in nine of ten lots. Ethephon in the dark had similar or greater germination percentages than water with light. Ethephon with light improved germination in three of ten lots compared with ethephon in the dark. The effect of cold, moist stratification in comparison with darkness varied by seed lot. Five lots of E. purpurea (L.) Moench were tested; however, no treatment differences were measured. The finding that ethethon promoted E. angustifolia and E. pallida seed germination in darkness could be useful in the cultivation of these two species. Chemical name used: 2-chloroethylphosphonic acid (ethephon).
PMCID: PMC1626658  PMID: 17075609
17.  Patterns of Variation in Alkamides and Cichoric Acid in Roots and Aboveground Parts of Echinacea purpurea (L.) Moench 
We investigated patterns of variation in alkamides and cichoric acid accumulation in the roots and aboveground parts of Echinacea purpurea (L.) Moench. These phytochemicals were extracted from fresh plant parts with 60% ethanol and quantified by high performance liquid chromatography (HPLC) analysis. Concentrations of alkamides and cichoric acid were measured on a dry-weight basis (mg·g−1). For total alkamides, concentrations among individual plants varied from 5.02 to 27.67 (mean = 14.4%) in roots, from 0.62 to 3.42 (mean = 1.54) in nearly matured seed heads (NMSH), and 0.22 to 5.25 (mean = 0.77) in young tops (about ½ flower heads, ¼ leaves, and ¼ stems). For cichoric acid, concentrations among individual plants varied from 2.65 to 37.52 (mean = 8.95), from 2.03 to 31.58 (mean = 10.9), and from 4.79 to 38.55 (mean = 18.88) in the roots, the NMSH, and the tops, respectively. Dodeca-2E, 4E, 8Z, 10E-tetraenoic acid isobutylamide and dodeca-2E, 4E, 8Z, 10Z-tetraenoic acid isobutylamide (alkamides 8/9) accounted for only 9.4% of the total alkamides in roots, but comprised 87.9% in the NMSH, and 76.6% in the young tops. Correlations of concentrations of alkamides or cichoric acid between those of roots and those of the NMSH were not statistically significant, and either within the roots, the NMSH, and the young tops. However, a significant negative correlation was observed between the concentration of cichoric acid in the roots and in young tops, and a significant positive correlation was observed between total alkamide concentration in the roots and cichoric acid concentration in the young tops. These results may be useful in the genetic improvement of E. purpurea for medicinal use.
PMCID: PMC1317087  PMID: 16429598
medicinal plants; phytochemicals; HPLC; correlation; plant breeding
18.  Chromosome Karyotypes of Echinacea angustifolia var. angustifolia and E. purpurea 
Chromosome karyotypes of the most commonly cultivated and medicinally used Echinacea taxa, E. angustifolia DC. var. angustifolia and E. purpurea (L.) Moench., were analyzed. The chromosomes of both taxa are medium in length, ranging from 4.12 to 5.83 μm in E. angustifolia var. angustifolia and 3.99 to 6.08 μm in E. purpurea. No abrupt length changes in the chromosomes were noted. The karyotypes of the two species are generally similar, but a distinguishable feature exists in one pair of chromosomes. The centromere of chromosome pair 10 is subterminally located in E. purpurea, but terminally located in E. angustifolia var. angustifolia, which can be readily recognized in mitotic metaphase cell plates. This finding may provide useful information for Echinacea evolutionary, genetic, and breeding studies.
PMCID: PMC1317084  PMID: 16429596
medicinal plants; chromosome variation
19.  Commercial Seed Lots Exhibit Reduced Seed Dormancy in Comparison to Wild Seed Lots of Echinacea purpurea 
Seed germination patterns were studied in E. purpurea (L.) Moench grouped by seed source, one group of seven lots from commercially cultivated populations and a second group of nine lots regenerated from ex situ conserved wild populations. Germination tests were conducted in a growth chamber in light (40 μmol·m−2·s−1) or darkness at 25 °C for 20 days after soaking the seeds in water for 10 minutes. Except for two seed lots from wild populations, better germination was observed for commercially cultivated populations in light (90% mean among seed lots, ranging from 82% to 95%) and in darkness (88% mean among seed lots, ranging from 82% to 97%) than for wild populations in light (56% mean among seed lots, ranging from 9% to 92%) or in darkness (37% mean among seed lots, ranging from 4% to 78%). No germination difference was measured between treatments in light and darkness in the commercially cultivated populations, but significant differences were noted for treatments among wild populations. These results suggest that repeated cycles of sowing seeds during cultivation without treatments for dormancy release resulted in reduced seed dormancy in E. purpurea.
PMCID: PMC1317083  PMID: 16429595
medicinal plants; seed germination; plant selection and breeding
20.  Correction: Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture 
Genome Biology  2005;6(8):403.
A correction to Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture by L Li, X Wang, M Xia, V Stolc, N Su, Z Peng, S Li, J Wang, X Wang and XW Deng. Genome Biology 2005, 6:R52
PMCID: PMC1273630
21.  Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture 
Genome Biology  2005;6(6):R52.
A transcriptome analysis of chromosome 10 of 2 rice subspecies identifies 549 new gene models and gives experimental evidence for around 75% of the previously unsupported predicted genes.
Sequencing and annotation of the genome of rice (Oryza sativa) have generated gene models in numbers that top all other fully sequenced species, with many lacking recognizable sequence homology to known genes. Experimental evaluation of these gene models and identification of new models will facilitate rice genome annotation and the application of this knowledge to other more complex cereal genomes.
We report here an analysis of the chromosome 10 transcriptome of the two major rice subspecies, japonica and indica, using oligonucleotide tiling microarrays. This analysis detected expression of approximately three-quarters of the gene models without previous experimental evidence in both subspecies. Cloning and sequence analysis of the previously unsupported models suggests that the predicted gene structure of nearly half of those models needs improvement. Coupled with comparative gene model mapping, the tiling microarray analysis identified 549 new models for the japonica chromosome, representing an 18% increase in the annotated protein-coding capacity. Furthermore, an asymmetric distribution of genome elements along the chromosome was found that coincides with the cytological definition of the heterochromatin and euchromatin domains. The heterochromatin domain appears to associate with distinct chromosome level transcriptional activities under normal and stress conditions.
These results demonstrated the utility of genome tiling microarray in evaluating annotated rice gene models and in identifying novel transcriptional units. The tiling microarray sanalysis further revealed a chromosome-wide transcription pattern that suggests a role for transposable element-enriched heterochromatin in shaping global transcription in response to environmental changes in rice.
PMCID: PMC1175972  PMID: 15960804
22.  CSN1 N-Terminal–dependent Activity Is Required for Arabidopsis Development But Not for Rub1/Nedd8 Deconjugation of Cullins: A Structure-Function Study of CSN1 Subunit of COP9 Signalosome 
Molecular Biology of the Cell  2002;13(2):646-655.
The COP9 signalosome (CSN) is a multifunctional protein complex essential for arabidopsis development. One of its functions is to promote Rub1/Nedd8 deconjugation from the cullin subunit of the Skp1-cullin-F-box ubiquitin ligase. Little is known about the specific role of its eight subunits in deneddylation or any of the physiological functions of CSN. In the absence of CSN1 (the fus6 mutant), arabidopsis CSN complex cannot assemble, which destabilizes multiple CSN subunits and contributes, together with the loss of CSN1, to the phenotype of fus6. To distinguish CSN1-specific functions, we attempted to rescue the complex formation with deletion or point-mutation forms of CSN1 expressed as transgenes in fus6. We show that the central domain of CSN1 is critical for complex assembly, whereas the C-terminal domain has a supporting role. By expressing the C231 fragment, which contains the structural information but lacks the presumed functional domain located at the N terminus, we have rescued the complex formation and restored the Rub1/Nedd8 deconjugation activity on cullins (fus6/C231). Nonetheless, fus6/C231 exhibits pleiotropic phenotype, including photomorphogenic defects and growth arrest at seedling stage. We conclude that CSN1 N-terminal domain is not required for the Rub1/Nedd8 deconjugation activity of cullins, but contributes to a significant aspect of CSN functions that are essential for plant development.
PMCID: PMC65656  PMID: 11854419

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