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ABSTRACT: Green colored fibers and white colored fibers sequencing of upland cotton

PROVIDER: PRJNA565616 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10121900_1.fastq.gz	Fastqsanger.gz
	SRR10121900_2.fastq.gz	Fastqsanger.gz
	SRR10121901_1.fastq.gz	Fastqsanger.gz
	SRR10121901_2.fastq.gz	Fastqsanger.gz
	SRR10121902_1.fastq.gz	Fastqsanger.gz

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Comparison of cotton fiber to ovule at 9 DPA

Project description:RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule. RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule.

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Proteomics analysis reveal flavonoid biosynthesis and starch and sucrose metabolism pathway are involved in pigmentation of brown cotton fibers

Project description:Naturally brown-colored upland cotton is used in specific textile industries. The color results from condensed tannin formed by proanthocyanidin (PA) oxidation. However, the roles of PA biosynthesis and glucose metabolism in brown pigmentation are unclear. Here, we integrated proteomes and metabolomes of fibers collected at 0, 10, 20 and 30 days post-anthesis (DPA) from a brown-colored cotton line (Z161) and its near-isogenic white-colored cotton line (RT). Compared with in RT, all the proteins in the flavonoid biosynthetic pathway in Z161 were highly accumulated. The metabolome data showed that the epi-flavan-3-ols in most of the brown fibers. Significantly lower levels of catalytic enzymes of the starch and sucrose metabolic pathway, which affects cellulose biosynthesis, were found in Z161 compared with in RT, except endoglucanase and uridine-5'-diphosphate (UDP)-D-glucose pyrophosphorylase

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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.

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Project description:Compare the expression profiles of natural brown and green cotton fibers, and white color fiber at 0 and 12 days post-anthesis (DPA) to identify genes involved in pigment synthesis

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Comparison of cotton fiber to ovule at 9 DPA

Project description:RNAs from the upland cotton 9-DPA fibers were compared to the 9-DPA fiber-detached ovule. Keywords: tissue comparison

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Project description:A cDNA library from 0-10 day post anthesis cotton ovules was established to study genes expressed in cotton ovule during initiation and quickly elongation period. We randomly sequenced over 100,000 ESTs from this library and acquired a gene pool of more than 28,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of about 28000 high-quality cotton cDNAs (with average length>750bp) and external controls. To study the different growth potential of cotton fibers in a one-year cycle, we then hybridized the array with RNA samples derived from +7 DPA wild-type upland cotton fibers in four different seasons, respectively.

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Project description:To identify potential miRNAs involved in fiber development and elucidate their expression differences between G. barbadense and G. hirsutum, we constructed two small RNA libraries, Gb10 and Gh10, prepared from fibers of 3-79 (G. barbadense) and TM-1 (G. hirsutum) collected at 10 days post-anthesis (DPA). We identified 28 conserved miRNA families, including 24 that exactly match known plant miRNA families in miRBase. With MIREAP and newly developed software miRsearcher, 7 candidate-novel miRNAs were found. 5 candidate-novel miRNAs were expressed in both species, 2 candidate-novel miRNAs were expressed only in one species. Moreover, 4 miRNA families showed significant expression differences between sea-island cotton and upland cotton in 10 DPA fibers.

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