Plant Omics最新文献_第4页

Mining and characterization of Allium cepa expressed sequence tags (ESTs) encoding receptor-like kinases (RLKs) 编码受体样激酶(RLKs)的葱表达序列标签(ESTs)的挖掘与鉴定

Plant Omics Pub Date : 2018-05-20 DOI: 10.21475/POJ.11.02.18.1250

S. Nanda

引用次数: 2

Metabolomics analysis of mangosteen (Garcinia mangostana Linn.) fruit pericarp using different extraction methods and GC-MS 不同提取方法及GC-MS对山竹果皮代谢组学分析

Plant Omics Pub Date : 2018-05-01 DOI: 10.21475/POJ.11.02.18.PNE1191

Siti Farah Mamat, Kamalrul Azlan Azizan, S. Baharum, N. Noor, W. Aizat

{"title":"Metabolomics analysis of mangosteen (Garcinia mangostana Linn.) fruit pericarp using different extraction methods and GC-MS","authors":"Siti Farah Mamat, Kamalrul Azlan Azizan, S. Baharum, N. Noor, W. Aizat","doi":"10.21475/POJ.11.02.18.PNE1191","DOIUrl":"https://doi.org/10.21475/POJ.11.02.18.PNE1191","url":null,"abstract":"Garcinia mangostana Linn. (mangosteen) reportedly contains several bioactive metabolites which have been used in various traditional disease treatment, nutritional supplement and skincare products. However, reports detailing its characterization and metabolite content are still scarce. Most of the earlier reports only focused on the extraction of specific metabolites such as xanthones and anthocyanins, rather than a comprehensive metabolome profile. In this study, global metabolomics approach using gas chromatography-mass spectrometry (GC-MS) analysis was conducted to profile the metabolite content of mangosteen fruit pericarp harvested at the final stage of ripening (dark purple stage). Five different extraction methods, which vary in their solvent mixtures, solvent ratios, with or without sonication were compared, aimed to maximize metabolite detection from the mangosteen tissue. The results showed that the method using a combined solvent mixture of methanol/chloroform/water (3:1:1 v/v ratio) with sonication has consistent reproducibility amongst biological replicates and successfully yielded the highest number of metabolites compared to the other methods. By combining the results of different extraction methods, we tentatively identified a total of 73 metabolites comprising of sugars (49.32%), alcohols (9.59%), sugar acids (8.22%), organic acids (6.85%), phenolic acids (5.48%), aromatic compounds (2.74%) and aldehyde (1.37%). This finding provides an overview of the metabolite content of mangosteen pericarp and comprehensive assessment of extraction methods for an untargeted metabolomics approach of this beneficial fruit.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"89-97"},"PeriodicalIF":0.0,"publicationDate":"2018-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42144282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Transcriptome and gene expression analysis revealed mechanisms for producing high oleoresin yields from Simao pine (Pinus kesiya var. langbianensis) 转录组和基因表达分析揭示了思毛松(Pinus kesiya var. langbianensis)高产油树脂的机制

Plant Omics Pub Date : 2018-02-20 DOI: 10.21475/POJ.11.01.18.PNE1085

W. Yi., Yuan Xiaolong, Hua Mei, Li Jiang, W. Juan

{"title":"Transcriptome and gene expression analysis revealed mechanisms for producing high oleoresin yields from Simao pine (Pinus kesiya var. langbianensis)","authors":"W. Yi., Yuan Xiaolong, Hua Mei, Li Jiang, W. Juan","doi":"10.21475/POJ.11.01.18.PNE1085","DOIUrl":"https://doi.org/10.21475/POJ.11.01.18.PNE1085","url":null,"abstract":"Simao pine (Pinus kesiya Royle ex Gordon var. langbianensis (A. Chev.) Gaussen) is an important oleoresin source in Yunnan Province, China. However, the molecular mechanisms of high oleoresin yield from Simao pine remain unclear. In this study, RNA-Seq was used to investigate the transcriptome of the species and compare the gene expression profiles of wounded bark from high and low oleoresin-yielding individuals, and the expression levels of genes in the methyl-erythritol 4-phosphate (MEP) pathway were detected by qPCR. A total of 1.41 billion reads were obtained and assembled into 68,881 unigenes from samples of the wounded bark of Simao pine. The KEGG analysis of differentially expressed genes showed that MEP pathway genes were obviously differentially expressed, while most genes in the mevalonate (MVA) pathway were not. The qPCR analysis showed that the MEP pathway gene expression of wounded bark from high oleoresin-yielding genotypes was higher than that of low oleoresin-yielding genotypes. The gene expression differences of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), and geranylgeranyl pyrophosphate synthase (GGPPs) between high and low oleoresin-yielding genotypes were significant. This implies that DXS, HDR, and GGPPs play important roles in high oleoresin production in Simao pine.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"42-49"},"PeriodicalIF":0.0,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46954734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Transcriptome analysis of Arabidopsis to predict stress length-specific regulatory networks involved in drought response 拟南芥转录组分析预测干旱反应中的胁迫长度特异性调控网络

Plant Omics Pub Date : 2018-02-20 DOI: 10.21475/poj.11.01.18.pne735

S. Akhtartavan, M. Talebi

{"title":"Transcriptome analysis of Arabidopsis to predict stress length-specific regulatory networks involved in drought response","authors":"S. Akhtartavan, M. Talebi","doi":"10.21475/poj.11.01.18.pne735","DOIUrl":"https://doi.org/10.21475/poj.11.01.18.pne735","url":null,"abstract":"Drought stress is one of the major environmental factors impairing crops productivity worldwide. Plants use various regulatory genes to reprogram genome activities to cope with such stresses. Among regulatory genes, transcription factors (TFs) function as terminal transducers and directly regulate the expression of wide spectrum of downstream genes. Multiplicity of the TF families and the complex interactions between TFs and cis-elements on the promoters of target genes as well as cross-talk between TFs in response to stress indicate the complexity of signaling networks involved in plant stress responses. This study aimed to use computational and statistical approaches to analyze a microarray dataset from Arabidopsis which covering different time periods of drought stress. After identifying and functional grouping of differentially expressed gens (DEGs), genes encoded TFs were determined and networked based on gene set enrichment analysis (GSE). Hierarchical regulatory network in each condition was assigned. After that, networks were used to conduct network topology analysis. Results indicated an obvious orientation in genome activity toward response to different cues; energy homeostasis and photosynthesis stability was occurred under drought stress. Also, 3787, 2931 and 5115 genes were differentially expressed under the early, moderate and prolonged drought stress, respectively, among them, 169, 140 and 261 TF were identified. Analysis of constructed regulatory networks of each drought condition revealed that plant recruits different but somewhat overlapping strategies to cope with stress in a long period of time. In each drought period, specific or common signaling pathways are activated using several numbers of transcription factors. It seems that among all identified TFs, ARR5, ARR6, ABF3, MYB29, MYB76 and SIGs genes are good candidate to manipulate plant stress tolerance.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47703369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Comparative transcriptome analysis of two Gerbera hybrida cultivars revealed cold tolerance mechanism 两个非洲菊品种的比较转录组分析揭示了其抗寒机制

Plant Omics Pub Date : 2018-02-20 DOI: 10.21475/POJ.11.01.18.PNE874

Shen-chong Li, Qinli Shan, Rongpei Yu, A. N. Siddique, Xia Li, Chunmei Yang, Jiwei Ruan, Mingyang Li

{"title":"Comparative transcriptome analysis of two Gerbera hybrida cultivars revealed cold tolerance mechanism","authors":"Shen-chong Li, Qinli Shan, Rongpei Yu, A. N. Siddique, Xia Li, Chunmei Yang, Jiwei Ruan, Mingyang Li","doi":"10.21475/POJ.11.01.18.PNE874","DOIUrl":"https://doi.org/10.21475/POJ.11.01.18.PNE874","url":null,"abstract":"Temperature is one of central factors that shape the distribution and growth pattern of Gerbera hybrida. The cultivars of this species have vast variation in the morphology and stress adaptation. In the current study, comparative transcriptome analysis of two haploid cultivars with discriminative phenotype, i.e., Gerbera hybrida Hongjixing and Gerbera hybrida Qiuri, was used to uncover differentially expressed functional unigenes using an Illumina Hiseq2000 sequencing platform. Through high-throughput cDNA sequencing (RNA-seq), we generated 99160 UniGenes from 19.09G primary reads with an average length of 978 bp and an N50 equaling 1620. It was filtered by Trimmomatic and assembled by Trinity. A total of 58127 transcripts were functional annotated by mapping to five protein databases by BLASTX, with topmost differently expressed unigenes (DEGs) directed to transcriptional regulation, secondary metabolism and stress response, etc. Cold treatment (-2°C) of haploid seedlings in intelligent cooled incubator had adverse effects on both cultivars, which was more serious in Qiuri which was exhibited by the lower chlorophyll fluorescence after cold treatment, compared to Hongjixing. This indicates the better cold tolerance of Hongjixing. The qRT-PCR result indicated that besides common pathways, novel pathways like latex biosynthesis potentially contributes to the better cold tolerance of Hongjixing. In view of the ubiquity of cold temperature, this study provided new insights into the mechanism dissection and guidance for cold stress condition.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"10-19"},"PeriodicalIF":0.0,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42582751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Isolation and characterization of Rep PepYLCV encoding gene from West Sumatra 西苏门答腊岛Rep PepYLCV编码基因的分离与鉴定

Plant Omics Pub Date : 2018-02-20 DOI: 10.21475/poj.11.01.18.pne1055

Bastian Nova, E. Syafriani, A. Asben, J. Jamsari

引用次数: 1

Dynamic roles of microRNAs in nutrient acquisition and plant adaptation under nutrient stress: A review 微小RNA在营养胁迫下营养获取和植物适应中的动态作用：综述

Plant Omics Pub Date : 2018-02-20 DOI: 10.21475/POJ.11.01.18.PNE1014

R. Shahzad, P. W. Harlina, M. Ayaad, M. Ewas, E. Nishawy, S. Fahad, Hizar Subthain, M. Amar

引用次数: 16

An efficient heat-shock protocol for transformation of Agrobacterium rhizogenes without spontaneous generation to antibiotic resistance 一个有效的热冲击方案转化根农杆菌不自发产生抗生素耐药性

Plant Omics Pub Date : 2018-02-20 DOI: 10.21475/poj.11.01.18.pne918

Juan Manuel Jiménez-Antaño, J. Pérez-Vargas, A. Ariza-Castolo, Octavio Gómez Guzmán, Graciano Calva-Calva

{"title":"An efficient heat-shock protocol for transformation of Agrobacterium rhizogenes without spontaneous generation to antibiotic resistance","authors":"Juan Manuel Jiménez-Antaño, J. Pérez-Vargas, A. Ariza-Castolo, Octavio Gómez Guzmán, Graciano Calva-Calva","doi":"10.21475/poj.11.01.18.pne918","DOIUrl":"https://doi.org/10.21475/poj.11.01.18.pne918","url":null,"abstract":"Antibiotic resistance occurs when the use of antibiotics to treat bacterial infections or to select for transformed bacteria from in vitro cultures becomes ineffective. Although this phenomenon is primarily observed in medicine, it also affects the success of scientific research when bacterial-based genetic transformation experiments are performed. During the agrotransformation of plant cells, tissue, and organs, the acquisition of antibiotic resistance by Agrobacterium spp. has been widely observed, making it difficult to select for the transformed bacteria. The objective of this study was to develop a heat-shock protocol for the transformation of Agrobacterium rhizogenes without the spontaneous generation of antibiotic resistance, to increase its sensitivity and specificity to produce transgenic hairy roots. After the bacterium was transformed, it was cultured in liquid culture medium and plated on solid medium to isolate colonies. The genetic transformation of the bacteria and the plant tissue was verified by PCR and by β-glucuronidase assays. The reproducibility of the method was assessed among the A. rhizogenes strains LBA 9402, A4 and 15834 using streptomycin, kanamycin and ampicillin for selection.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"20-29"},"PeriodicalIF":0.0,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43124567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Role of sulphate (SO42-) in improvement the growth of rocket plants (Eruca sativa L.) under selenate (SeO42-) levels 硒酸盐(SO42-)水平下硫酸盐(SO42-)对火箭植物(Eruca sativa L.)生长的促进作用

Plant Omics Pub Date : 2018-02-20 DOI: 10.21475/POJ.11.01.18.PNE1112

A. Ali, A. Hassan, N. Saber, Eman G. El-Hosary

引用次数: 0

CrMYC1 transcription factor overexpression promotes the production of low abundance terpenoid indole alkaloids in Catharanthus roseus CrMYC1转录因子过表达可促进红花低丰度萜类吲哚类生物碱的产生

Plant Omics Pub Date : 2018-02-12 DOI: 10.21475/POJ.11.01.18.PNE1020

Sima Sazegari, A. Niazi, Farajollah Shahriari-Ahmadi, N. Moshtaghi, Y. Ghasemi

{"title":"CrMYC1 transcription factor overexpression promotes the production of low abundance terpenoid indole alkaloids in Catharanthus roseus","authors":"Sima Sazegari, A. Niazi, Farajollah Shahriari-Ahmadi, N. Moshtaghi, Y. Ghasemi","doi":"10.21475/POJ.11.01.18.PNE1020","DOIUrl":"https://doi.org/10.21475/POJ.11.01.18.PNE1020","url":null,"abstract":"Catharanthus roseus is known as the only source for the low-abundance anticancer agents namely vinblastine and vincristine. Fine tuning of accumulation of such secondary metabolites is highly governed by the regulatory genes. Among these genes, Catharanthus roseus MYC1 (CrMYC1) is known as one of the key transcription factors regulating the biosynthesis of terpenoid indole alkaloid metabolites in C. roseus. In this study, CrMYC1 coding sequence (AF283506) was isolated and cloned in PBI121 plant binary vector. Then, CrMYC1 was transiently overexpressed in C. roseus leaves using agroinfiltration method. In addition to molecular analysis for confirming CrMYC1 overexpression, the profile of some chief terpenoid indole alkaloids in control and transgenic plants was evaluated by HPLC to elucidate the role of CrMYC1 in an increased in the anticancer components. The results indicated that overexpression of CrMYC1 transcription factor can increase most important terpenoid indole alkaloids including vinblastine, vincristine, and catharanthine in C. roseus. HPLC analysis of catharanthine and vinblastine contents showed about 3 and 2.5 fold increases, respectively, while the increase in vinecristine was not significant compared to that of the control. Therefore, CrMYC1 is introduced as an efficient candidate for manipulating TIA pathway in C. roseus and increasing at least the most valuable terpenoid indole alkaloids in this plant.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"30-36"},"PeriodicalIF":0.0,"publicationDate":"2018-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42540919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9