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Transcriptome profiling of Gossypium hirsutum in response to NO by high-throughput tag-sequencing

ABSTRACT: Nitric oxide(NO) is emerging as an important signaling molecule with diverse physiological functions in plants, leading to a necessity to discover the downstream genes and signal transduction network modulated by NO. In the current study, changes in gene expression in response to NO were studied in upland cotton(Gossypium hirsutum) using Solexa/Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing method. After mapping to an integrated reference sequence database, we obtained about 30,000 genes per library, and yielded 2,393 differential expressed genes in total.

ORGANISM(S): Gossypium hirsutum

PROVIDER: GSE53674 | GEO | 2015/12/01

SECONDARY ACCESSION(S): PRJNA232622

REPOSITORIES: GEO

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cDNA microarray expression profile during fiber elongation between G. hirsutum and G. barbadense

2012-05-24 | GSE18028 | GEO

Cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation

Project description:As an initial step to explore the cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation, conventional heirloom G. hirsutum (Gh) cultivars [susceptible Acala SJ-2 (SJ2), moderately resistant Upland Wild Mexico Jack Jones (WMJJ), and resistant Acala NemX] that have been shown to be useful as an informative genetic model for detecting and introgressing RKN resistance genes into commercial Upland cotton were used to enlighten the molecular mechanisms and gene expression of RKN resistance. Using the next generation sequencing (NGS) Illumina MiSeq and HiSeq, we performed RNA-seq profiling in roots with disease progression of 10 days and collected from 23 days old plants of SJ2, WMJJ, and NemX. With three biological replicates of each treatment from each cultivar, plants were subjected to RKN-infestation and non-infested control developing a total of 18 RNA-seq libraries

2022-04-01 | GSE190503 | GEO

cDNA microarray expression profile during fiber elongation between G. hirsutum and G. barbadense

Project description:Sea-island cotton (Gossypium barbadense L.) has superior fiber quality properties such as length, fineness and strength, while Upland cotton (Gossypium hirsutum L.) is characterized by high yield. To reveal features of Upland cotton and Sea-island cotton fiber cells, differential genes expression profiles during fiber cell elongation and in secondary wall deposits were established using cDNA microarray technology. This research provides a valuable genomic resource to deepen our understanding of the molecular mechanisms of cotton fiber development, and may ultimately lead to improvements in cotton fiber quality and yield. 15 samples were prepared for microarray slides hybridized with three biological replicate samples including a swap-dye experiment for each growth stage. Each spot had a repeat in the microarray slideM-oM-<M-^Ltherefore, data for six replicate experiments performed with biologically independent samples.

2012-05-23 | E-GEOD-18028 | biostudies-arrayexpress

Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue and during fibre development stages.

Project description:This SuperSeries is composed of the following subset Series: GSE29566: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue. GSE29567: Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress during fibre development stages. Refer to individual Series

2012-06-03 | E-GEOD-29810 | biostudies-arrayexpress

Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense

2015-06-26 | GSE64958 | GEO

Transcriptomics and Metabolomics of 10 - 28 day post anthesis cotton fiber from Gossypium hirsutum and Gossypium barbadense

Project description:Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. Results from RNA-seq were combined with non-targeted metabolomics. Results: Approximately 38,000 transcripts were expressed (RPKM>2) in each fiber type and approximately 2,000 of these transcripts were differentially expressed in a cross-species comparison at each timepoint. Enriched Gene Ontology biological processes in differentially expressed transcripts suggested that Gh fibers were more stressed. Conclusions: Both metabolomic and transcriptomic data suggest that better mechanisms for managing reactive oxygen species contribute to the increased fiber length in Gossypium barbadense. This appears to result from enhanced ascorbate biosynthesis via gulono-1,4-lactone oxidase and ascorbate recycling via dehydroascorbate reductase. See Bioproject PRJNA263926 and SRA accession SRP049330 for study design and raw sequencing data and Bioproject PRJNA269608 and TSA accession GBYK00000000 for Gossypium arboreum assembled contig sequences used for transcriptome mapping - Cotton fiber mRNA from 10,15,18,21 and 28 day post anthesis fiber from either Gossypium hirusutm or Gossypium barbadense was sequenced and differential gene expression analysis was conducted between species for each timepoint and between adjacent timepoints. Each timepoint was representative of fiber from 9 individual plants processed as 3 biological replicate pools (material from 3 individual plants per pool).

2015-06-26 | E-GEOD-64958 | biostudies-arrayexpress

Gossypium hirsutum strain:upland cotton

Project description:Gossypium hirsutum strain:upland cotton Raw sequence reads

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Project description:Comparative RNA-Seq study of expression in Gossypium hirsutum nectaries

2018-04-19 | GSE113373 | GEO

Cotton fiber LC-MS/MS - Proteomic Analysis of Differences in Fiber Development between Wild and Cultivated Gossypium hirsutum L

Project description:Upland cotton (Gossypium hirsutum L.) is one of the world’s most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 day post-anthesis (DPA), 20 DPA and mature stages at the physiological level. In order to explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences and better inform our efforts to further enhance cotton fiber quality, an iTRAQ-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified, among them 336 were defined as differentially expressed proteins (DEPs) between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in Phenylpropanoid biosynthesis, Zeatin biosynthesis, Fatty acid elongation and other processes. Association analysis between transcroptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. The difference of proteomics had been verified at the mRNA level by qPCR, also at physiological and biochemical level by POD activity determination and ZA content estimation. This work corroborate the major pathways involved in cotton fiber development and demonstrate that POD activity and zeatin content have a great potential related to fiber elongation and thickening.

2017-08-28 | PXD006604 | Pride

Global gene expression analysis of cotton (Gossypium hirsutum L.) under drought stress in leaf tissue.

Project description:Transcriptome analysis in cotton under drought stress. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out in leaf tissue. Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Leaf samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. Gene expression profiles in drought induced and their respective control samples were analyzed using Affymertix cotton Genechip Genome arrays to study the global changes in the expression of genome.

2012-06-04 | GSE29566 | GEO

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