Plant Omics最新文献_第10页

Different tobacco cultivation regions lead to variations in tobacco leaf gene expression profiles involved in carbonhydrate metabolism and ion transportation 烟叶碳水化合物代谢和离子转运相关基因的表达谱在不同的种植区域存在差异

Plant Omics Pub Date : 2016-08-20 DOI: 10.21475/poj.16.09.04.pne32

Liming Lu, Wen-yu Xu, Yong Chen, Zong-xiang Tang, Lei Liu, Liqin Li

{"title":"Different tobacco cultivation regions lead to variations in tobacco leaf gene expression profiles involved in carbonhydrate metabolism and ion transportation","authors":"Liming Lu, Wen-yu Xu, Yong Chen, Zong-xiang Tang, Lei Liu, Liqin Li","doi":"10.21475/poj.16.09.04.pne32","DOIUrl":"https://doi.org/10.21475/poj.16.09.04.pne32","url":null,"abstract":"Tobacco is an important crop economically in China, and tobacco quality varies across its cultivated regions. To unveil the mechanisms that result in such varied tobacco leaf qualities, we have analyzed the tobacco leaf gene expression profiles of four areas in Sichuan province, China. Tobacco leaves in the 12 position were collected from plants in four different regions, namely Huili, Miyi, Xingwen and Jiange, and submitted for microarray analysis. Gene expression levels from Miyi group were used as control, and that from Jiange, Xingwen and Huili were compared to Miyi group respectively. A total of 5154 differentially expressed genes (DEGs) were detected, among which 2731 genes were up-regulated and 2423 genes were down-regulated. Based on gene ontology (GO) analysis, significant DEGs were classified into 15 categories (P≤0.05) based on properties pertaining to transferase activity, transmembrane transporter activity, binding, transcription regulator activity, metabolic processes, secondary metabolic processes, etc. Our results also show that these DEGs were significantly enriched in 11 pathways, including metabolic pathways, starch and sucrose metabolism, photosynthesis, etc. Our study suggests that many of the genes involved in various plant physiological and biochemical processes significantly differed across these four different regions, which may explain their differences in tobacco leaf quality.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"233-239"},"PeriodicalIF":0.0,"publicationDate":"2016-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68659197","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: 0

De novo transcriptome sequencing and analysis of Hydrilla verticillata (L.f.) Royle 水螅verticillata (L.f.)从头转录组测序及分析罗伊尔

Plant Omics Pub Date : 2016-08-20 DOI: 10.21475/POJ.16.09.04.P7882

E. Goyal, Singh Amit Kumar, R. Singh, A. Mahato, K. Kanika

{"title":"De novo transcriptome sequencing and analysis of Hydrilla verticillata (L.f.) Royle","authors":"E. Goyal, Singh Amit Kumar, R. Singh, A. Mahato, K. Kanika","doi":"10.21475/POJ.16.09.04.P7882","DOIUrl":"https://doi.org/10.21475/POJ.16.09.04.P7882","url":null,"abstract":"Hydrilla verticillata (L.f.) Royle, an aquatic plant, best documented example of an inducible C4 photosynthetic system, which concentrates CO2 in the chloroplasts without enzymatic compartmentation in mesophyll and bundle sheath cells. H. verticillata is a facultative C4 plant, which shifts from C3 to C4 photosynthesis under certain conditions, but lacks Kranz anatomy. Little is known about the molecular changes required for the transition to the C4 carbon concentrating mechanism (CCM). To gain insight into the processes that are involved in the C3 to the C4 transition, high throughput transcriptome sequencing and analysis were carried out using 454-GS FLX Titanium technology. A total of 533,595 reads were obtained after quality filtering. From these reads, 1,813 “Expressed sequence tags (ESTs)” were generated yielding 1,538 unigenes. Almost 95% of these unigenes aligned to the “Nonredundant (nr)” database, whereas 4.88% did not show homology to any other known gene. “Reads per kilobase per million sequenced reads (RPKM)” analysis indicated that 283 unigenes were up-regulated and 383 unigenes were down-regulated in the C4 state as compared to the C3 state. A number of transcription factors found in our study were involved in photosynthesis. These consisted of, HAP3/NF-YB, AP/EREBP and C2H2 family. GO, COG and KEGG analysis indicated that many genes were involved in energy metabolism, nucleotide metabolism, photosynthesis, signal transduction, stress responses and are worthy of further investigation. This transcriptome analysis is an important first step towards understanding the molecular changes underpinning the transition from the C3 to the C4 photosynthesis in H. verticillata. It could also be a useful genomic resource for engineering C4 photosynthetic CCM in C3 crops.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"270-280"},"PeriodicalIF":0.0,"publicationDate":"2016-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658970","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

Characterization of a pumpkin mRNA encoding a Cyclin-Dependent Protein Kinase (CDK) potentially involved in phloem development 编码周期蛋白依赖性蛋白激酶(CDK)的南瓜mRNA的表征可能参与韧皮部发育

Plant Omics Pub Date : 2016-06-20 DOI: 10.21475/POJ.16.09.03.PNE114

Paul Starsky Herrera-Pola, Roberto Toscano-Morales, Roberto Ruiz

{"title":"Characterization of a pumpkin mRNA encoding a Cyclin-Dependent Protein Kinase (CDK) potentially involved in phloem development","authors":"Paul Starsky Herrera-Pola, Roberto Toscano-Morales, Roberto Ruiz","doi":"10.21475/POJ.16.09.03.PNE114","DOIUrl":"https://doi.org/10.21475/POJ.16.09.03.PNE114","url":null,"abstract":"The phloem is involved in the delivery of nutrients but also of long-range signals that regulate diverse processes. Several different RNAs have been found in the phloem translocation stream, which could have a role in signaling. In a previous work, we have found several RNAs in pumpkin phloem sap exudates in response to viral infection, among them a transcript encoding a potential cyclindependent protein kinase (CDK). In this study, we report the further characterization of the aforementioned CDK mRNA. The complete sequence of this mRNA, which we termed CmCDKP (for Cucurbita maxima CDK from Phloem), was obtained (GenBank no. AIQ82912.1). The phylogenetic analysis of the virtual translation of this sequence showed that CmCDKP is closely related to those involved in transcriptional regulation via RNA polymerase II CTD phosphorylation, or splicing control. The mRNA accumulated to highest levels in pollen tissue. Interestingly, the mRNA localized to the companion cell-sieve element complex in the phloem, developing phloem, and also in isolated cells in the shoot apical meristem, suggesting a role in early phloem development.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"213-219"},"PeriodicalIF":0.0,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658420","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

Isolation and molecular characterization of a novel Na + /H + antiporter gene, AlNHX2, from Aeluropus littoralis and comparison of AlNHX1 and AlNHX2 滨海海蛸Na + /H +反向转运基因AlNHX2的分离与分子表征及AlNHX1与AlNHX2的比较

Plant Omics Pub Date : 2016-06-20 DOI: 10.21475/POJ.16.09.03.PNE35

Zahra Sami, A. Alemzadeh

{"title":"Isolation and molecular characterization of a novel Na + /H + antiporter gene, AlNHX2, from Aeluropus littoralis and comparison of AlNHX1 and AlNHX2","authors":"Zahra Sami, A. Alemzadeh","doi":"10.21475/POJ.16.09.03.PNE35","DOIUrl":"https://doi.org/10.21475/POJ.16.09.03.PNE35","url":null,"abstract":"Halophytes have high tolerance against salinity and it is expected that these plants have special proteins that allow them to thrive under salinity conditions. Hence, to understand molecular aspects of vacuolar Na + /H + antiporter, which has a possible role in salt tolerance in halophytic plants, a novel Na + /H + antiporter gene, AlNHX2, was isolated and characterized by rapid amplification of cDNA ends (RACE) technique. The results revealed that AlNHX2 is expressed in leaves, stems and roots and its expression in leaves is 1.767 and 1.269 times higher than stems and roots, respectively. This gene has an ORF with 1617 bp in length, a 3'-UTR region with 245 pb, and a 5'-UTR region with 187 bp which encodes a 538 amino acid protein shared a high homology with those putative vacuolar Na + /H + antiporters of higher plants. Putative phosphorylation sites within AlNHX1 and AlNHX2 were determined using the prediction software, and the binding of 14-3-3 protein to specific domains within AlNHX1 and AlNHX2 was predicted. The results also revealed this binding is induced by a protein kinase-mediated phosphorylation of a specific Thr or Ser residue in these domains. The results also revealed that the activities of AlNHX1 and AlNHX2 are regulated by PKC, p38MAPK and GSK3. In addition, the findings reported here show the interaction of CaM protein with C-terminal of AlNHX2. Autoinhibitory domain at C-terminal region of AlNHX2 that can suppress the protein activity under normal growth conditions was also found.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"205-212"},"PeriodicalIF":0.0,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658569","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

The role of sucrose metabolizing proteins in hyperosmotic stress tolerance in sweet sorghum (Sorghum bicolor L. Moench) 蔗糖代谢蛋白在甜高粱耐高渗胁迫中的作用

Plant Omics Pub Date : 2016-06-20 DOI: 10.21475/POJ.16.09.03.P7724

A. Njokweni, O. Ibraheem, B. Ndimba

{"title":"The role of sucrose metabolizing proteins in hyperosmotic stress tolerance in sweet sorghum (Sorghum bicolor L. Moench)","authors":"A. Njokweni, O. Ibraheem, B. Ndimba","doi":"10.21475/POJ.16.09.03.P7724","DOIUrl":"https://doi.org/10.21475/POJ.16.09.03.P7724","url":null,"abstract":"Sugar accumulation is a common metabolic response under drought stress conditions. However, studies on the underlying molecular mechanisms of sugar accumulation under stress remain restricted. This study explores the role of sucrose metabolizing proteins in conferring tolerance to drought-induced hyperosmotic stress, and ultimately osmotic adjustment in sorghum. The effect of stress on sugar content, enzyme activity and gene expression was investigated. Sweet sorghum varieties (ICSV213 and ICSB338) differing in levels of drought tolerance were subjected to a 10-day water deficit period. Brix plant sap analysis indicated elevated total soluble sugar levels under water stress conditions in both varieties with ICSV213 demonstrating a higher brix content than ICSB338. HPLC analysis gave a decrease in sucrose levels and an increase in glucose and fructose concentrations in both varieties with ICSV213 demonstrating higher hexose levels. Enzyme activity levels of invertase, sucrose phosphate synthase and sucrose synthase were found to increase under stress in both varieties with ICSV213 invertase displaying the highest activity when compared to other sucrose metabolizing enzymes. Transcriptional expression of invertase and sucrose phosphate synthase (SPS) genes was significantly up regulated in ICSV213 under stressed conditions, whereas sucrose synthase (Susy) levels remained low in both varieties. Data obtained for sorghum variety ICSV213 points towards a relationship between hyperosmotic stress tolerance and the accumulation of solutes and sucrose metabolism proteins. Consequently variety ICSV213 may therefore be an excellent target for future development of hyperosmotic stress tolerant sweet sorghum.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"183-190"},"PeriodicalIF":0.0,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658250","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: 2

Genome-wide transcriptome profiling of Gossypium spp. roots during early growth after infection with Rotylenchulus reniformis 感染肾形轮虫后棉根生长早期的全基因组转录组分析

Plant Omics Pub Date : 2016-06-20 DOI: 10.21475/POJ.16.09.03.P7816

Y. Tilahun

{"title":"Genome-wide transcriptome profiling of Gossypium spp. roots during early growth after infection with Rotylenchulus reniformis","authors":"Y. Tilahun","doi":"10.21475/POJ.16.09.03.P7816","DOIUrl":"https://doi.org/10.21475/POJ.16.09.03.P7816","url":null,"abstract":"Plant-nematode interactions have been studied extensively. The identification of genes expressed in root organs subsequent to nematode infection have been studied to a lower extent. Fewer still, potential resistance genes have been identified in cotton towards Rotylenchulus reniformis the reniform nematode (RN). Currently, there have been three cotton genomes completely sequenced. Gossypium, or cotton, genomes sequenced include: Gossypium hirsutum cv TM1, Gossypium arboreum, and Gossypium raimondii. This study imparts knowledge of differentially expressed genes (DEGs) after individual domesticated and wild cotton plants have been infected with approximately 50,000 juvenile RNs. After extraction of Total RNA from infected roots and subsequent next generation 454 pyrosequencing methods were employed, FastQC quality control measures were completed prior to Trimomatic-0.32 trimming from 33,788 reads, resulting in a significant decrease in the number of input reads (3454 input reads or DEGs). Putative descriptions were made for 634 input reads or DEGs, many of which were repeated multiple times as predicted proteins/enzymes or partials. The definition of 52 DEGs were made and enriched through the assignment of gene ontology (GO) terms that highlight categories of host plant genes for potential targets in future downstream transformation of cotton plants, especially those involved in strengthening systemic acquired resistance (SAR) or the hypersensitive response (HR) that occurs most often in plants when in defense against pathogen attack. This study reveals known protein/enzymes (52), unknown protein/enzymes (582) and unassigned DEGs (2820).","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"198-204"},"PeriodicalIF":0.0,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658329","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: 0

Molecular modeling and docking studies of phytoalexin(s) with pathogenic protein(s) as molecular targets for designing the derivatives with anti-fungal action on Alternaria spp. of Brassica 植物抗菌素(phytoalexin)的分子模拟及与致病蛋白的对接研究，为设计抗油菜Alternaria spp.的衍生物提供分子靶点

Plant Omics Pub Date : 2016-06-20 DOI: 10.21475/POJ.16.09.03.P7654

R. Pathak, G. Taj, D. Pandey, V. Kasana, M. Baunthiyal, Anil Kumar

{"title":"Molecular modeling and docking studies of phytoalexin(s) with pathogenic protein(s) as molecular targets for designing the derivatives with anti-fungal action on Alternaria spp. of Brassica","authors":"R. Pathak, G. Taj, D. Pandey, V. Kasana, M. Baunthiyal, Anil Kumar","doi":"10.21475/POJ.16.09.03.P7654","DOIUrl":"https://doi.org/10.21475/POJ.16.09.03.P7654","url":null,"abstract":"The present study used molecular modeling and docking based approaches to test some proteins viz, ABC transporter, Amr1, Beta-tubulin, Cutinase, Fusicoccadiene synthase and Glutathione transferase of 'Alternaria brassicicola' as possible molecular target of phytoalexins during pathogenesis or defense response. Molecular Operating Environment (MOE) was used to predict 3D structures of above proteins which were subsequently docked with phytoalexins which included Camalexin, Brassilexin, Rutalexin and Spirobrassinin by Molegro Virtual Docker. The results of molecular docking of Spirobrassinin with the above targets showed greater affinity as revealed from binding energy in the range of -73.09 to -94.46 Kcal/mol. Accordingly five derivatives of Spirobrassinin were further designed and docked against each target proteins, so as to detect phytoalexin(s) having the antifungal potential. The molecular modeling and docking experiments identified two derivatives of Spirobrassinins, with binding energy in the range of -77.50 to -85.88 Kcal/mol respectively, which could be used for protection of 'Brassica' plants against infection by 'Alternaria spp' including 'Alternaria brassicicola' and 'Alternaria' brassicae, main pathogen of 'Alternaria' blight in rapeseed mustard. Further studies and downstream validation would give way to use the above phytoalexin(s) as a substitute for hazardous fungicides to control plant diseases.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"172-182"},"PeriodicalIF":0.0,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658653","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: 17

Microsatellites mining in date palm (Phoenix dactylifera L.) and their cross transferability across Arecaceae family 枣椰树微卫星的挖掘及其在槟榔科植物间的可转移性

Plant Omics Pub Date : 2016-06-20 DOI: 10.21475/POJ.16.09.03.P7793

K. P. Manju, R. Manimekalai, S. Naganeeswaran, V. Arunachalam, A. Karun

{"title":"Microsatellites mining in date palm (Phoenix dactylifera L.) and their cross transferability across Arecaceae family","authors":"K. P. Manju, R. Manimekalai, S. Naganeeswaran, V. Arunachalam, A. Karun","doi":"10.21475/POJ.16.09.03.P7793","DOIUrl":"https://doi.org/10.21475/POJ.16.09.03.P7793","url":null,"abstract":"Phoenix dactylifera L. (date palm) is the first publicly available nuclear genome sequence under Arecaceae family and indeed under the entire order Arecales. These genomic sequences were mined for microsatellites which could be used for marker assisted selection for important traits. We have developed an integrated, configurable and time effective microsatellite mining and annotation pipeline for this purpose. Microsatellite survey of date palm whole genome shotgun sequences using the developed pipeline detected a total of 166,760 perfect repeats with an average of one SSR per 2.2kb. Putative functions of these SSR-containing sequences within the proximity of genic regions were predicted. Primers targeting the functionally important SSR regions were designed and a set of eight SSR primers synthesized and were validated in vitro across five members of the Arecaceae family (coconut, arecanut, oilpalm, date palm and palmyrah palm). We have found that 28.6% of the SSRs are common among the members of arecaceae family. Those SSRs could be used in molecular marker analysis of less studied palm family members like arecanut and palmyrah palm.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"191-197"},"PeriodicalIF":0.0,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658288","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

Overexpression of potato transcription factor (StWRKY1) conferred resistance to Phytophthora infestans and improved tolerance to water stress 马铃薯转录因子(StWRKY1)的过表达增强了对疫霉的抗性，提高了对水分胁迫的耐受性

Plant Omics Pub Date : 2016-03-10 DOI: 10.21475/POJ.160902.P7649X

R. Shahzad, P. W. Harlina, Xie Cong-hua, M. Ewas, E. Nishawy, Pan Zhenyuan, Moatzbellah Mohamed Foly

{"title":"Overexpression of potato transcription factor (StWRKY1) conferred resistance to Phytophthora infestans and improved tolerance to water stress","authors":"R. Shahzad, P. W. Harlina, Xie Cong-hua, M. Ewas, E. Nishawy, Pan Zhenyuan, Moatzbellah Mohamed Foly","doi":"10.21475/POJ.160902.P7649X","DOIUrl":"https://doi.org/10.21475/POJ.160902.P7649X","url":null,"abstract":"Potato (Solanum tuberosum) late blight caused by oomycete Phytophthora infestans (Pi) is highly destructive to potato yield and cost huge losses each year. Regulation of a network of transcription machinery, controlled by transcription factors (TF’s), is required to overcome the susceptibility. WRKY TF’s are known to regulate transcription machinery upon biotic and abiotic stresses in different crop plants. We cloned and characterized a WRKY gene, StWRKY1, from potato cDNA synthesized from Pi infested leaves. StWRKY1 protein localized typically in the nucleus. Overexpression (OE) of StWRKY1 positively regulates Pi resistance as well as drought tolerance in transgenic potato. The elevated resistance in OE lines was co-related with higher accumulation of pathogenesis-related (PR) genes as compared to untransformed control plants. Interestingly, increased susceptibility of co-suppression (CSP) plants was associated with down regulation of PR genes expression. Moreover, transgenic lines overexpressing StWRKY1 showed tolerance in terms of less rate of water loss, during dehydration assay. Importantly, expression of StWRKY1 was upregulated upon treatment with plant hormones, suggesting its involvement in basal signal transduction pathway. Overall, our findings provided evidence that StWRKY1 positively regulate biotic and abiotic stress resistance thereby modulating plant basal defense networks, thus play a significant role for crop improvement.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"149-158"},"PeriodicalIF":0.0,"publicationDate":"2016-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68659532","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

An efficient method for isolating large quantity and high quality RNA from oleaginous microalgae for transcriptome sequencing 从产油微藻中分离大量高质量RNA进行转录组测序的有效方法

Plant Omics Pub Date : 2016-03-10 DOI: 10.21475/POJ.160902.P7617X

Anongpat Suttangkakul, Piyada Juntawong, A. Sirikhachornkit, Chonlada Yaisumlee, Kanidtha Jariyachawalid, K. Kangwansaichol, S. Apisitwanich, S. Vuttipongchaikij

{"title":"An efficient method for isolating large quantity and high quality RNA from oleaginous microalgae for transcriptome sequencing","authors":"Anongpat Suttangkakul, Piyada Juntawong, A. Sirikhachornkit, Chonlada Yaisumlee, Kanidtha Jariyachawalid, K. Kangwansaichol, S. Apisitwanich, S. Vuttipongchaikij","doi":"10.21475/POJ.160902.P7617X","DOIUrl":"https://doi.org/10.21475/POJ.160902.P7617X","url":null,"abstract":"Transcriptome analysis requires a large quantity of high-quality DNase-treated RNA for poly(A)+ mRNA isolation and sequencing. This could be problematic in many oleaginous microalgal species that harbor strong cell walls and accumulate high lipid content. Using Scenedesmus obliquus, a microalga with high oil content and potential as a source of algal biofuel, we assessed the efficiency of four RNA isolation methods: direct extraction using TriPure, mechanical breakage using either freeze-thawed with bead beating or grinding in liquid nitrogen followed by TriPure, and grinding in liquid nitrogen before using Qiagen RNeasy Plant Mini Kit. Liquid nitrogen grinding with TriPure method gave the best RNA yields at 15.15 µg mg -1 cell dry weight and ~148.9 µg total RNA from 100 ml culture of S. obliquus. Despite lower yields, RNA isolation of oil accumulating cells (~22% w/w lipid content) provided ~68.1 µg total RNA with the yield of 1.70 µg mg -1 cell dry weight. Transcriptome sequencing and de novo assembly with the average contig length of 824 bp reflected high quality of RNA obtained using this method. The RNA isolation protocol was tested on six other oleaginous microalgae including Chlamydomonas reinhardtii, S. acuminatus, Chorella vulgaris, Chlorococcum humicola, Tetradesmus cumbricus and Coelastrum sp. and yielded 0.86 - 5.42 µg mg -1 cell dry weight. For large scale RNA isolation from microalgae, grinding with liquid nitrogen before TriPure provided the best yield and quality. This finding helps simplify RNA isolation for upcoming transcriptome analyses in microalgae.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"9 1","pages":"126-135"},"PeriodicalIF":0.0,"publicationDate":"2016-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68659017","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