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ABSTRACT: RNase-seq of dormant buds in 'Fuji' apple

PROVIDER: PRJNA1138898 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29923180_1.fastq.gz	Fastqsanger.gz
	SRR29923180_2.fastq.gz	Fastqsanger.gz
	SRR29923181_1.fastq.gz	Fastqsanger.gz
	SRR29923181_2.fastq.gz	Fastqsanger.gz
	SRR29923182_1.fastq.gz	Fastqsanger.gz

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Project description:LncRNA-seq of dormant buds in 'Fuji' apple (Malus × domestica)

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The identification of small RNAs differentially expressed in apple buds reveals a potential role of the miR159-MYB regulatory module during dormancy

Project description:Winter dormancy is an adaptative mechanism that temperate and boreal trees have developed to protect their meristems against low temperatures. In apple trees (Malus domestica), cold temperatures induce bud dormancy at the end of summer/beginning of the fall. Apple buds stay dormant during winter until they are exposed to a period of cold, after which they can resume growth (budbreak) and initiate flowering in response to warm temperatures in spring. It is well-known that small RNAs modulate temperature responses in many plant species, but however, how small RNAs are involved in genetic networks of temperature-mediated dormancy control in fruit tree species remains unclear. Here, we have made use of a recently developed ARGONAUTE (AGO)-purification technique to isolate small RNAs from apple buds. A small RNA-seq experiment resulted in the identification of small RNAs that change their pattern of expression in apple buds during dormancy.

2021-11-30 | GSE189658 | GEO

Apple SWATH-MS - Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value

Project description:Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown. Here, we reported a bud sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation. Quantitative SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) proteomics investigations revealed proteome changes in the apple red skin bud mutation and a total of 411 differentially expressed proteins were identified in apple skin. The mutant showed significantly increased expression levels of photosynthesis-related proteins, stress-related proteins as well as anthocyanins biosynthesis pathway. On the other hand, substanial downregulation of mitogen-activated protein kinase 4 (MAPK4) and mevalonate kinase (MVK) were detected. We also hypothesize that a post-transcriptional regulation of the skin color formation occurs in the mutant through the advanced SWATH-MS analysis. Overall, our work provide important information on the application of proteomic methods for analysing proteomes changes in Fuji apple and highlights a clade of regulatory proteins potentially contributed to the fruit skin color formation.

2019-06-18 | PXD011132 | Pride

RNA-SEQ raw data of apple phlomes at bud breaking stage

Project description:In order to understand the role of phloems of apple dwarfing rootstocks,and investigated the expression differences of dwarfing and vigorous apple stocks in the bud break stage, The phloem tissue at bud break stage(0 DABB(days after buds break) of three apple rootstocks including A1d（a partial GA insensitive mutant of Malus hupehensis ),WT Malus hupehensis and were QZ1(a hybrid of Malus hupensis and a Cylindrical apple variety) were sampled and underwent RNA-Seq analysis.

2024-10-24 | GSE276181 | GEO

The expression differences in different kinds of 60 DABB(Days after buds break) apple rootstock phloem tissue

Project description:in order to understand the role of phloems of apple dwarfing rootstocks,and investigated the expression differences of dwarfing and vigorous apple stocks in the phloem tissue at active growing stage. The phloem tissue at active growing stage(60 DABB(days after buds break) of three apple dwarfing rootstocks including M9,B9,A1d（a partial GA insensitive mutant of Malus hupensis）and two vigorous apple rootstock PYTC ( WT of Malus hupensis) and M. sylvestris were sampled and underwent RNA-Seq analysis.

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Project description:transcriptome analysis of Fuji apple

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Project description:Genome assemblies of 'Fuji' apple

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Small RNA-sequencing from apple in phase transition

Project description:We performed Illumina sequencing of sRNA libraries prepared from juvenile and reproductive phase buds from the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and 6 novel members displayed significant differential expression (DE) patterns in juvenile and reproductive stages. The study provides new insight into our understanding of fundamental mechanism of poorly studied phase transitions in apple and other woody plants and important resource for future in-depth research in the apple development.

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