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Gossypium

ABSTRACT: DNA methylation in cotton evolution

PROVIDER: PRJNA314138 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3219090_1.fastq.gz	Fastqsanger.gz
	SRR3219090_2.fastq.gz	Fastqsanger.gz
	SRR3219100_1.fastq.gz	Fastqsanger.gz
	SRR3219100_2.fastq.gz	Fastqsanger.gz
	SRR3219110_1.fastq.gz	Fastqsanger.gz

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Gossypium hirsutum

Project description:DNA methylation dynamics during cotton ovule and fiber development [ncRNA-Seq]

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Gossypium hirsutum

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Gossypium

Project description:Insight into structure variations and evolution of allopolyploidy cotton genomes

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Identification of anther expressing genes in cotton (Gossypium hirsutum)

2013-10-31 | GSE51779 | GEO

Identification of anther expressing genes in cotton (Gossypium hirsutum)

Project description:This study was initiated with the objective of identifying the anther/tapetum specific promoters from cotton floral buds. Cotton is an important commercial crop. Hybrid cotton varieties are developed to obtain improved yield and fiber quality. Most of the hybrid seed production in cotton is carried out by hand emasculation, which requires large amount of manpower, resulting in high cost of hybrid seed. We are developing barnase-barstar based male sterility system, which would be a better alternative for hybrid development. The tapetum specific promoters are main requirement for such a system. The study was thus carried out to identify genes expressed in the anthers. Cotton bud sizes were correlated with tapetum development. RNA was isolated from following tissues: • Anther tissues from buds at pre-meiotic stage of development (Tapetum absent) • Buds without anther tissues at pre-meiotic stage of development • Anther tissues from buds during meiosis (Tapetum present) • Buds without anther tissues during meiosis • Anther tissues from buds at post-meiotic stage of development (Tapetum degenerated) • Buds without anther tissues at post-meiotic stage of development • Leaf tissues • Seedling 5 days after germination Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following Affymetrix protocols. Three biological replicates were maintained.

2013-10-31 | E-GEOD-51779 | biostudies-arrayexpress

Affymetrix Cotton Genome array expression data of cotton fiber at different developmental stages from different varieties of Gossypium hirsutum

Project description:Cotton fiber were used for the expression analysis at different developmental stages Affymetrix Cotton Genome array were used for the global profiling of gene expression of cotton fiber at different developmental stages

2012-03-20 | GSE36228 | GEO

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

DNA methylation dynamics during cotton ovule and fiber development [ncRNA-Seq]

Project description:DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. Genome-wide bisulfite -, mRNA-, and small RNA-sequencing analyses reveal that CHH hypermethyaltion through RdDM in euchromatin is associated with expression changes of nearby genes in ovules. The ovule-derived fiber cells not only maintain euchromatic CHH hypermethylation, but also generate additional heterochromatic CHH hypermethylation independent of RdDM. Moreover, CHG and CHH methylation in promoter and transcribed regions contribute to the expression bias of homoeologous genes in the allotetraploid cotton. This epigenetic and expression dynamics of developmental regulation could provide a molecular basis for natural selection and domestication of plants and animals.

2016-01-21 | GSE61761 | GEO

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