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1.
Plant Genome ; 11(3)2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30512040

RESUMO

Ginger ( Roscoe), a perennial herb, is one of the most economically valuable plants in the Zingiberaceae family. Gingerol, as the major constituents of ginger essential oil, contributes to the unique flavor and pharmaceutical value of ginger. However, the pathway of gingerol biosynthesis has not been verified and described in ginger to help understand the biosynthesis of secondary metabolites in nonmodel species. In this study, the concentrations of gingerols were quantified at different stages of rhizome development and in different tissues. The results confirmed that rhizomes are the major source of gingerols and that accumulation of gingerols in the rhizome starts at an early developmental stage. We also assembled a reference ginger transcriptome, which is composed of 219,479 unigenes consisting of 330,568 transcripts and provides a high-quality genetic resource for further research. An analysis of differentially expressed genes (DEGs) identified 12,935 DEGs among several different comparisons. Five genes [ (), (), p (), O (), and ()] associated with gingerol biosynthesis were identified as being significantly differentially expressed in the rhizome at an early developmental stage and all five genes were upregulated. Expression analysis revealed that different loci of these genes have become functionally specialized in different tissues and different developmental stages of the rhizome (subfunctionalization). Among the DEGs, and may act as gatekeepers and rate-limiting enzymes in the gingerol biosynthesis pathway and thus play an important role in regulating the biosynthesis of gingerol.


Assuntos
Catecóis/metabolismo , Álcoois Graxos/metabolismo , Gengibre/metabolismo , Perfilação da Expressão Gênica , Genes de Plantas , Gengibre/genética , Rizoma/metabolismo
2.
Plant Physiol Biochem ; 132: 547-556, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30316164

RESUMO

Ginger (Zingiber officinale Roscoe), one of the most economically valuable plants in the Zingiberaceae family, is widely used as a spice and flavoring agent for beverages, bakery, confectionary, and pharmaceutics. Bacterial wilt disease, caused by Ralstonia solanacearum, is one of the most detrimental production constraints in ginger cultivation. Field cultivation experiments indicated that soil moisture affects the incidence of bacterial wilt disease. However, the relationship between soil moisture and bacterial wilt incidence as well as the mechanism that underlie this infection remain unclear. This study confirms that high soil moisture elevates the susceptibility to R. solanacearum infection; transcriptome sequencing was performed to elucidate the underlying mechanisms. Differential expression indicates that a small number of genes is involved in both the response to high soil moisture as well as post successful R. solanacearum infection; furthermore, a large number of genes is involved in the defense of the infection. In response to high soil moisture, higher ABA contents, and higher expression levels of ABF4 may be related to higher tiller density in ginger. More importantly, WAK16 and WAK3-2 may be determinative genes that weaken the resistance to R. solanacearum in ginger under high soil moisture. The down-regulated expression levels of PRX, CPY, and XET genes indicate that in response to successful R. solanacearum infection, the normal cell wall metabolism may be disturbed and the hypersensitive response may be inhibited. In summary, our study deepens our understanding of the molecular mechanisms of the soil moisture dependent wilt susceptibility of ginger.


Assuntos
Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Gengibre/genética , Gengibre/microbiologia , Umidade , Doenças das Plantas/microbiologia , Ralstonia solanacearum/patogenicidade , Solo , Parede Celular/metabolismo , Suscetibilidade a Doenças , Gengibre/crescimento & desenvolvimento , Anotação de Sequência Molecular , Doenças das Plantas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Análise de Sequência de RNA , Transcriptoma/genética
3.
BMC Genomics ; 19(1): 692, 2018 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-30241497

RESUMO

BACKGROUND: Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species Zingiber kawagoii and Z. shuanglongensis was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of in situ ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses. RESULTS: Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in Z. kawagoii and no nucleotide substitution but only indels found in Z. shuanglongensis. Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species, Z. kawagoii and Z. shuanglongensis were estimated to be diverged since 218~ 238 thousand generations ago (complete divergence since 41.5~ 43.5 thousand generations ago). This time is more recent than the time of Taiwan Island formation. In addition, high proportion of differential expression genes (DEGs) is non-polymorphic or non-positively selected, suggesting key roles of plastic genetic divergence in broaden the selectability in incipient speciation. While some positive selected DEGs were mainly the biotic and abiotic stress-resistance genes, emphasizing the importance of adaptive divergence of stress-related genes in sympatric ecological speciation. Furthermore, the higher proportional expression of functional classes in Z. kawagoii than in Z. shuanglongensis explains the more widespread distribution of Z. kawagoii in Taiwan. CONCLUSIONS: Our results contradict the previous hypothesis of independent origination of these two island endemic ginger species from SE China and SW China. Adaptive divergent responses to the stress explain how these gingers maintain genetic differentiation in sympatry. However, the recent speciation and rapid expansion make extremely low intraspecific genetic variation in these two species. This study arise a more probable speciation hypothesis of sympatric speciation within an island via the mutation-order mechanism underlying the same environmental pressure.


Assuntos
Adaptação Fisiológica , Especiação Genética , Gengibre/genética , Mutação , Proteínas de Plantas/genética , Polimorfismo de Nucleotídeo Único , Estresse Fisiológico , Genética Populacional , Gengibre/classificação , Sequenciamento de Nucleotídeos em Larga Escala , RNA de Plantas , Simpatria
4.
Chemosphere ; 201: 137-143, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29524814

RESUMO

The presence of antibiotic residues in vegetables has been highlighted as a risk to human health; antibiotics not only cause toxic effects to plants but can also induce antibiotic resistance gene (ARG) expression. Using a soil-free approach, this study aimed to explore the response of ginger growth to tetracycline (TC) pollution and to assess the levels of antibiotic residues in different plant organs and the presence of ARGs in the rhizome. Ginger growth in a highly TC-contaminated environment was remarkably inhibited. Photosynthetic parameters, fluorescence parameters, and some physiological indicators (oxidative substances, photosynthetic pigments, enzyme activity, etc.) were negatively influenced by TC contamination. Although the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activity levels significantly increased, their effects appear to be limited. The accumulation of TC in the rhizome (28.1 mg kg-1) was greater than that in the roots, stem, or leaves. All tested antibiotic resistance genes except for tetL were detectable in the rhizome, and their relative abundance was in the order integron1>tetG > tetA > tetC > tetB > tetM. The level of TC in ginger rhizomes was much higher than the maximum residue limits. The potential dose of TC acquired from the consumption of ginger grown in a highly TC-contaminated environment poses no obvious risk to adults but may be a threat to children.


Assuntos
Antibacterianos/toxicidade , Resistência Microbiana a Medicamentos/genética , Gengibre , Poluentes do Solo/toxicidade , Tetraciclina/toxicidade , Antibacterianos/metabolismo , Transferência Genética Horizontal , Genes Bacterianos , Gengibre/efeitos dos fármacos , Gengibre/genética , Gengibre/crescimento & desenvolvimento , Rizoma/genética , Solo/química , Poluentes do Solo/metabolismo , Tetraciclina/metabolismo
5.
Zhongguo Zhong Yao Za Zhi ; 43(3): 493-501, 2018 Feb.
Artigo em Chinês | MEDLINE | ID: mdl-29600613

RESUMO

The NAC family is an important transcription factor which regulate plant growth and development, signal transduction, and stress response.In this study, the protein identification, subfamily classification, the determination of physical and chemical properties, protein structure, and expression pattern of NAC family were performed using bioinformatic methods based on the RNA-seq data of ginger. The results showed that a total of 72 NAC transcription factors were identified in 271.1 Mb total nucleotides, and they could be clustered into 13 subfamilies according to the phylogenetic tree.The physical and chemical properties, structure analysis revealed that the amino acid number and isoelectric point were different among 13 NAC subfamilies; the secondary structure of NACs transcription factors mainly consist of random coil, and the tertiary structure is similar.In addition,the expression patterns of genes under different soil moisture and Ralstonia solanacearum infection showed that 23 NACs were differentially expressed, which were mainly distributed in Ⅷ,Ⅶ, and ⅩⅤ subfamilies related to plant senescence, hormone metabolism and cell wall metabolism.The results provide some valuable information for the research and development of NAC transcription factors in ginger.


Assuntos
Gengibre/genética , Proteínas de Plantas/genética , RNA de Plantas/genética , Fatores de Transcrição/genética , Regulação da Expressão Gênica de Plantas , Família Multigênica , Filogenia , Estrutura Terciária de Proteína , Análise de Sequência de RNA
6.
PLoS One ; 12(3): e0173489, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28301540

RESUMO

The Amami Island group of the Ryukyu Archipelago, Japan, harbors extensive species diversity of Asarum in a small landmass. The fine-scale population genetic structure and diversity of nine insular endemic Asarum species were examined using nuclear DNA microsatellite loci and ITS sequences. High population genetic diversity (HS = 0.45-0.79) was estimated based on the microsatellites, implying outcrossing of Asarum species within populations accompanied by inbreeding. Bayesian clustering analyses revealed that species were divided into three robust genetic clusters and that the species within each cluster had a homogeneous genetic structure, indicating incomplete lineage sorting. This conclusion was supported by an ITS phylogeny. The degree of genetic differentiation among species was very low both within and between clusters (FST = 0.096-0.193, and 0.096-0.266, respectively). Although species can be crossed artificially to produce fertile hybrids, our results indicate that there is very little evidence of hybridization or introgression occurring among species in the wild, even within stands composed of multiple sympatric species. The highly differentiated floral morphology of the studied species is likely to impose reproductive isolation between them and maintain their integrity in the wild. A lack of genetic differentiation between sympatric species suggests that speciation within this group occurred rapidly and recently.


Assuntos
Flores/fisiologia , Genes de Plantas , Gengibre/classificação , Biodiversidade , Gengibre/genética , Japão , Filogenia , Especificidade da Espécie
7.
Genetica ; 144(6): 627-638, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27722803

RESUMO

Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.


Assuntos
Análise do Polimorfismo de Comprimento de Fragmentos Amplificados , Marcadores Genéticos/genética , Variação Genética , Gengibre/genética , Cruzamento , Gengibre/citologia , Filogenia
8.
Mol Biol Rep ; 43(12): 1347-1358, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27585572

RESUMO

Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.


Assuntos
Gengibre/genética , Polimorfismo Genético , Animais , DNA de Plantas/genética , Marcadores Genéticos , Humanos , Repetições de Microssatélites , Filogenia , Análise de Sequência de DNA
9.
Mol Phylogenet Evol ; 103: 55-63, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27400627

RESUMO

Species can arise via the divisive effects of allopatry as well as due to ecological and/or reproductive character displacement within sympatric populations. Two separate lineages of Costaceae are native to the Neotropics; an early-diverging clade endemic to South America (consisting of ca. 16 species in the genera Monocostus, Dimerocostus and Chamaecostus); and the Neotropical Costus clade (ca. 50 species), a diverse assemblage of understory herbs comprising nearly half of total familial species richness. We use a robust dated molecular phylogeny containing most of currently known species to inform macroevolutionary reconstructions, enabling us to examine the context of speciation in Neotropical lineages. Analyses of speciation rate revealed a significant variation among clades, with a rate shift at the most recent common ancestor of the Neotropical Costus clade. There is an overall predominance of allopatric speciation in the South American clade, as most species display little range overlap. In contrast, sympatry is much higher within the Neotropical Costus clade, independent of node age. Our results show that speciation dynamics during the history of Costaceae is strongly heterogeneous, and we suggest that the Costus radiation in the Neotropics arose at varied geographic contexts.


Assuntos
Gengibre/classificação , Animais , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Especiação Genética , Gengibre/genética , Filogenia , Filogeografia , Folhas de Planta/genética , Análise de Sequência de DNA
10.
Carbohydr Polym ; 151: 474-479, 2016 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-27474591

RESUMO

The ability of chitosan and oligochitosan to enhance ginger (Zingiber officinale) resistance to rhizome rot caused by Fusarium oxysporum in storage was investigated. Both chitosan and oligochitosan at 1 and 5g/L significantly inhibited rhizome rot, with the best control at 5g/L. Chitosan and oligochitosan applied at 5g/L also reduced weight loss, measured as a decrease in fresh weight, but did not affect soluble solids content or titratable acidity of rhizomes. The two compounds applied at 5g/L induced ß-1,3-glucanase and phenylalanine ammonia-lyase enzyme activity and the transcript levels of their coding genes, as well as the total phenolic compounds in rhizome tissues. Therefore, the ability of chitosan and oligochitosan to reduce rot in stored rhizomes may be associated with their ability to induce defense responses in ginger. These results have practical implications for the application of chitosan and oligochitosan to harvested ginger rhizomes to reduce postharvest losses.


Assuntos
Quitina/análogos & derivados , Fusarium/efeitos dos fármacos , Gengibre/efeitos dos fármacos , Doenças das Plantas/prevenção & controle , Rizoma/efeitos dos fármacos , Quitina/farmacologia , Fusarium/fisiologia , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Gengibre/enzimologia , Gengibre/genética , Gengibre/microbiologia , Glucana 1,3-beta-Glucosidase/genética , Glucana 1,3-beta-Glucosidase/metabolismo , Fenilalanina Amônia-Liase/genética , Fenilalanina Amônia-Liase/metabolismo , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Rizoma/enzimologia , Rizoma/genética , Rizoma/microbiologia
11.
Methods Mol Biol ; 1391: 403-26, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27108333

RESUMO

Ginger is a rhizomatous plant that belongs to the family Zingiberaceae. It is a herbaceous perennial but cultivated as annual, with crop duration of 7-10 months. Ginger is native to India and Tropical South Asia. The tuberous rhizomes or underground stems of ginger are used as condiment, an aromatic stimulant, and food preservative as well as in traditional medicine. Ginger is propagated vegetatively with rhizome bits as seed material. Cultivation of ginger is plagued by rhizome rot diseases, most of which are mainly spread through infected seed rhizomes. Micropropagation will help in production of disease-free planting material. Sexual reproduction is absent in ginger, making recombinant breeding very impossible. In vitro technology can thus become the preferred choice as it can be utilized for multiplication, conservation of genetic resources, generating variability, gene transfer, molecular tagging, and their utility in crop improvement of these crops.


Assuntos
Gengibre/crescimento & desenvolvimento , Melhoramento Vegetal/métodos , Rizoma/crescimento & desenvolvimento , Sementes/crescimento & desenvolvimento , Criopreservação/métodos , Meios de Cultura/metabolismo , Técnicas de Cultura/métodos , DNA de Plantas/genética , DNA de Plantas/isolamento & purificação , Gengibre/embriologia , Gengibre/genética , Organogênese Vegetal , Reguladores de Crescimento de Planta/metabolismo , Plantas Geneticamente Modificadas/embriologia , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Rizoma/embriologia , Rizoma/genética , Sementes/embriologia , Sementes/genética , Transformação Genética
12.
Gene ; 575(2 Pt 2): 570-576, 2016 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-26392033

RESUMO

MicroRNAs (miRNAs) are a large family of endogenous small RNAs derived from the non-protein coding genes. miRNA regulates the gene expression at the post-transcriptional level and plays an important role in plant development. Zingiber officinale is an important medicinal plant having numerous therapeutic properties. Its bioactive compound gingerol and essential oil posses important pharmacological and physiological activities. In this study, we used a homology search based computational approach for identifying miRNAs in Z. officinale. A total of 16 potential miRNA families (miR167, miR407, miR414, miR5015, miR5021, miR5644, miR5645, miR5656, miR5658, miR5664, miR827, miR838, miR847, miR854, miR862 and miR864) were predicted in ginger. Phylogenetic and conserved analyses were performed for predicted miRNAs. Thirteen miRNA families were found to regulate 300 target transcripts and play an important role in cell signaling, reproduction, metabolic process and stress. To understand the miRNA mediated gene regulatory control and to validate miRNA target predictions, a biological network was also constructed. Gene ontology and pathway analyses were also done. miR5015 was observed to regulate the biosynthesis of gingerol by inhibiting phenyl ammonia lyase (PAL), a precursor enzyme in the biosynthesis of gingerol. Our results revealed that most of the predicted miRNAs were involved in the regulation of rhizome development. miR5021, miR854 and miR838 were identified to regulate the rhizome development and the essential oil biosynthesis in ginger.


Assuntos
Biologia Computacional/métodos , Gengibre/genética , MicroRNAs/genética , RNA de Plantas/genética , Regulação da Expressão Gênica de Plantas , MicroRNAs/metabolismo , Família Multigênica , Filogenia , RNA de Plantas/metabolismo , Rizoma/genética , Rizoma/crescimento & desenvolvimento , Homologia de Sequência do Ácido Nucleico
13.
Gene ; 566(2): 184-8, 2015 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-25895474

RESUMO

Zingiber officinale, medicinally the most important species within Zingiber genus, contains 6-gingerol as the active principle. This compound obtained from rhizomes of Z.officinale, has immense medicinal importance and is used in various herbal drug formulations. Our record of variation in content of this active principle, viz. 6-gingerol, in land races of this drug plant collected from different locations correlated with our Gene expression studies exhibiting high Chalcone Synthase gene (Chalcone Synthase is the rate limiting enzyme of 6-gingerol biosynthesis pathway) expression in high 6-gingerol containing landraces than in the low 6-gingerol containing landraces. Sequencing of Chalcone Synthase cDNA and subsequent multiple sequence alignment revealed seven SNPs between these contrasting genotypes. Converting this nucleotide sequence to amino acid sequence, alteration of two amino acids becomes evident; one amino acid change (asparagine to serine at position 336) is associated with base change (A→G) and another change (serine to leucine at position 142) is associated with the base change (C→T). Since asparagine at position 336 is one of the critical amino acids of the catalytic triad of Chalcone Synthase enzyme, responsible for substrate binding, our study suggests that landraces with a specific amino acid change viz. Asparagine (found in high 6-gingerol containing landraces) to serine causes low 6-gingerol content. This is probably due to a weak enzyme substrate association caused by the absence of asparagine in the catalytic triad. Detailed study of this finding could also help to understand molecular mechanism associated with variation in 6-gingerol content in Z.officinale genotypes and thereby strategies for developing elite genotypes containing high 6-gingerol content.


Assuntos
Aciltransferases/genética , Catecóis/metabolismo , Álcoois Graxos/metabolismo , Gengibre/metabolismo , Polimorfismo de Nucleotídeo Único , Sequência de Aminoácidos , Sequência de Bases , Primers do DNA , DNA de Plantas , Gengibre/genética , Dados de Sequência Molecular , Reação em Cadeia da Polimerase em Tempo Real
14.
PLoS One ; 9(12): e114134, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25461565

RESUMO

Alpinia genus are known generally as ginger-lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS-box genes in floral identity. In this study, four AP1/AGL9 MADS-box genes were cloned from Alpinia hainanensis, and protein-protein interactions (PPIs) and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1 lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6-like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL-AhSEP4, AhFUL-AhAGL6-like, AhFUL-AhSEP3b, AhSEP4-AhAGL6-like, AhSEP4-AhSEP3b, AhAGL6-like-AhSEP3b, and AhSEP3b-AhSEP3b) were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal-like or leaf-like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS-box genes.


Assuntos
Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Gengibre/genética , Proteínas de Plantas/metabolismo , Flores , Filogenia , Proteínas de Plantas/genética , Ligação Proteica
15.
PLoS One ; 9(10): e108581, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25333869

RESUMO

Plants from the Zingiberaceae family are a key source of spices and herbal medicines. Species identification within this group is critical in the search for known and possibly novel bioactive compounds. To facilitate precise characterization of this group, we have sequenced chloroplast genomes from species representing five major groups within Zingiberaceae. Generally, the structure of these genomes is similar to the basal angiosperm excepting an expansion of 3 kb associated with the inverted repeat A region. Portions of this expansion appear to be shared across the entire Zingiberales order, which includes gingers and bananas. We used whole plastome alignment information to develop DNA barcodes that would maximize the ability to differentiate species within the Zingiberaceae. Our computation pipeline identified regions of high variability that were flanked by highly conserved regions used for primer design. This approach yielded hitherto unexploited regions of variability. These theoretically optimal barcodes were tested on a range of species throughout the family and were found to amplify and differentiate genera and, in some cases, species. Still, though these barcodes were specifically optimized for the Zingiberaceae, our data support the emerging consensus that whole plastome sequences are needed for robust species identification and phylogenetics within this family.


Assuntos
Genoma de Cloroplastos , Gengibre/genética , Cloroplastos/genética , DNA de Plantas/análise , Gengibre/classificação , Sequenciamento de Nucleotídeos em Larga Escala , Repetições de Microssatélites , Anotação de Sequência Molecular , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Alinhamento de Sequência , Análise de Sequência de DNA
16.
PLoS One ; 9(6): e99731, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24940878

RESUMO

Bacterial wilt in ginger (Zingiber officinale Rosc.) caused by Ralstonia solanacearum is one of the most important production constraints in tropical, sub-tropical and warm temperature regions of the world. Lack of resistant genotype adds constraints to the crop management. However, mango ginger (Curcuma amada Roxb.), which is resistant to R. solanacearum, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to R. solanacearum, we have sequenced the transcriptome from wilt-sensitive ginger and wilt-resistant mango ginger using Illumina sequencing technology. A total of 26387032 and 22268804 paired-end reads were obtained after quality filtering for C. amada and Z. officinale, respectively. A total of 36359 and 32312 assembled transcript sequences were obtained from both the species. The functions of the unigenes cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. Large scale expression profiling showed that many of the disease resistance related genes were expressed more in C. amada. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either ginger or mango ginger. The identification of many defense related genes differentially expressed provides many insights to the resistance mechanism to R. solanacearum and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to R. solanacearum between ginger and mango ginger were identified. Finally, we have developed a web resource, ginger transcriptome database, which provides public access to the data. Our study is among the first to demonstrate the use of Illumina short read sequencing for de novo transcriptome assembly and comparison in non-model species of Zingiberaceae.


Assuntos
Curcuma/genética , Curcuma/microbiologia , Gengibre/genética , Gengibre/microbiologia , Doenças das Plantas/microbiologia , Ralstonia solanacearum/fisiologia , Transcriptoma/genética , Mapeamento de Sequências Contíguas , Bases de Dados Genéticas , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Genes de Plantas , MicroRNAs/genética , MicroRNAs/metabolismo , Anotação de Sequência Molecular , Doenças das Plantas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Análise de Sequência de RNA , Fatores de Transcrição/metabolismo , Regulação para Cima/genética
17.
Ann Bot ; 113(1): 119-33, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24280362

RESUMO

BACKGROUND AND AIMS: Zingiberales comprise a clade of eight tropical monocot families including approx. 2500 species and are hypothesized to have undergone an ancient, rapid radiation during the Cretaceous. Zingiberales display substantial variation in floral morphology, and several members are ecologically and economically important. Deep phylogenetic relationships among primary lineages of Zingiberales have proved difficult to resolve in previous studies, representing a key region of uncertainty in the monocot tree of life. METHODS: Next-generation sequencing was used to construct complete plastid gene sets for nine taxa of Zingiberales, which were added to five previously sequenced sets in an attempt to resolve deep relationships among families in the order. Variation in taxon sampling, process partition inclusion and partition model parameters were examined to assess their effects on topology and support. KEY RESULTS: Codon-based likelihood analysis identified a strongly supported clade of ((Cannaceae, Marantaceae), (Costaceae, Zingiberaceae)), sister to (Musaceae, (Lowiaceae, Strelitziaceae)), collectively sister to Heliconiaceae. However, the deepest divergences in this phylogenetic analysis comprised short branches with weak support. Additionally, manipulation of matrices resulted in differing deep topologies in an unpredictable fashion. Alternative topology testing allowed statistical rejection of some of the topologies. Saturation fails to explain observed topological uncertainty and low support at the base of Zingiberales. Evidence for conflict among the plastid data was based on a support metric that accounts for conflicting resampled topologies. CONCLUSIONS: Many relationships were resolved with robust support, but the paucity of character information supporting the deepest nodes and the existence of conflict suggest that plastid coding regions are insufficient to resolve and support the earliest divergences among families of Zingiberales. Whole plastomes will continue to be highly useful in plant phylogenetics, but the current study adds to a growing body of literature suggesting that they may not provide enough character information for resolving ancient, rapid radiations.


Assuntos
Filogenia , Plastídeos/genética , Zingiberales/genética , Evolução Biológica , Códon , Gengibre/genética , Modelos Genéticos , Dados de Sequência Molecular , Proteínas de Plantas/genética , Zingiberales/classificação
18.
BMC Plant Biol ; 13: 27, 2013 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-23410187

RESUMO

BACKGROUND: Ginger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric. RESULTS: In order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols. CONCLUSION: A significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific transcription factors and other regulatory genes were found that were common to the two species and that are excellent candidates for involvement in rhizome growth, differentiation and development. Large classes of enzymes involved in specialized metabolism were also found to have apparent tissue-specific expression, suggesting that gene expression itself may play an important role in regulating metabolite production in these plants.


Assuntos
Catecóis/metabolismo , Curcuma/metabolismo , Álcoois Graxos/metabolismo , Gengibre/metabolismo , Terpenos/metabolismo , Curcuma/genética , Etiquetas de Sequências Expressas , Gengibre/genética
19.
Am J Bot ; 100(3): 546-55, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23425560

RESUMO

PREMISE OF THE STUDY: Diversification of floral traits in angiosperms is often attributed to have been driven by adaptations to pollinators. Nevertheless, phylogenetic studies on the relationships among evolutionary changes in floral traits and pollination systems are still limited. We examined the relationships between floral trait changes and pollinator shifts in Bornean gingers (Zingiberaceae). These plants have strongly zygomorphic flowers pollinated by spiderhunter birds, bees of the genus Amegilla, and halictid bees. • METHODS: We identified pollination systems through field observations and recorded petal color, quantity of floral rewards, and seven measures of flower morphology in 28 ginger species. Phylogenetic trees were constructed from nucleotide sequences of the matK and ITS regions. We examined the correlations between the evolution of pollination systems and floral traits using phylogenetically independent contrasts. • KEY RESULTS: Significant association was found between pink color and spiderhunter pollination, orange and Amegilla pollination, and yellow and white and halictid pollination. Sugar production was higher in spiderhunter-pollinated species and lower in halictid-pollinated. Meanwhile, there was a significant association only for a subset of the floral morphological characters measured. Floral tube length, which is often thought to evolve to match the lengths of pollinator probing apparatuses, did not show any correlation. • CONCLUSIONS: There is considerable variation in the strength of association among pollination systems and floral traits. Lack of significant correlation in some traits could partly be explained by floral functions other than pollination, such as adaptations to prevent herbivore damage to the ovules. Further studies on these factors may improve understanding of plant-pollinator interactions.


Assuntos
Evolução Biológica , Flores/fisiologia , Gengibre/fisiologia , Polinização/fisiologia , Característica Quantitativa Herdável , Animais , Abelhas/fisiologia , Bornéu , DNA Intergênico , Flores/anatomia & histologia , Gengibre/genética , Filogenia , Análise de Componente Principal
20.
Gene ; 516(1): 58-65, 2013 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-23262347

RESUMO

Soft rot disease caused by the oomycete Pythium aphanidermatum (Edson) Fitzp. is the most economically significant disease of ginger (Zingiber officinale Rosc.) in tropical countries. All available ginger cultivars are susceptible to this pathogen. However a wild ginger relative viz., Zingiber zerumbet L. Smith, was identified as a potential soft rot resistance donor. In the present study, a putative resistance (R) gene designated, ZzR1 was isolated and characterized from Z. zerumbet using sequence information from Zingiber RGCs identified in our earlier experiments. Analysis of the 2280 bp segment revealed a 2157 bp open reading frame (ORF) encoding a putative cytoplasmically localized protein. The deduced ZzR1 protein shared high homology with other known R-genes belonging to the CC-NBS-LRR (coiled coil-nucleotide binding site-leucine rich repeat) class and had a calculated molecular weight of 84.61kDa. Real-time PCR analysis of ZzR1 transcription in Z. zerumbet following pathogen infection demonstrated activation at 3 hpi thus suggesting an involvement of ZzR1 in Z. zerumbet defense mechanism. Although many R-genes have been characterized from different taxa, none of them will help in the development of resistant ginger cultivars owing to the phenomenon of "Restricted Taxonomic Functionality" (RTF). Thus ZzR1 gene characterized from the resistant wild Zingiber accession represents a valuable genomic resource for ginger improvement programs. This first report on R-gene isolation from the Zingiber secondary gene pool is pivotal in designing strategies for engineering resistance in ginger, which is otherwise not amenable to conventional improvement programs owing to sexual reproduction barriers.


Assuntos
Genes de Plantas , Gengibre/genética , Imunidade Vegetal , Pythium/crescimento & desenvolvimento , Sequência de Aminoácidos , Clonagem Molecular , Primers do DNA , DNA de Plantas/genética , Regulação da Expressão Gênica de Plantas , Gengibre/imunologia , Gengibre/microbiologia , Dados de Sequência Molecular , Fases de Leitura Aberta , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Pythium/patogenicidade , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de DNA
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