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Comparative Methylome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety [Bisulfite-seq]

ABSTRACT: Comparative Methylome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety [Bisulfite-seq]

PROVIDER: PRJNA799770 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18183574_1.fastq.gz	Fastqsanger.gz
	SRR18183574_2.fastq.gz	Fastqsanger.gz
	SRR18183575_1.fastq.gz	Fastqsanger.gz
	SRR18183575_2.fastq.gz	Fastqsanger.gz
	SRR18183576_1.fastq.gz	Fastqsanger.gz

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Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

Project description:Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

| PRJNA799769 | ENA

Comparative Transcriptome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

Project description:We carried out the transcriptome analysis to identify the key genes involved in pear fruit semi-russet formation, by comparing the CK (russet) and bagging treated (green) ‘Cuiguan’ pear fruit skin 95 DAFB.

2020-10-31 | GSE153994 | GEO

Comparative Transcriptome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

2025-01-20 | GSE194228 | GEO

Comparative Methylome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety [Bisulfite-seq]

Project description:We carried out genomewide DNA methylation analysis by whole genome bisulfite sequencing to identify candidate genes involved in pear fruit semi-russet formation, by comparing the CK (russet) and bagging treated (green) ‘Cuiguan’ pear fruit skin 115 DAFB.

2025-02-25 | GSE194229 | GEO

Comparative Transcriptome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

Project description:Comparative Transcriptome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

| PRJNA644723 | ENA

Comparative Transcriptome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

Project description:Comparative Transcriptome Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

| PRJNA799771 | ENA

Analysis Reveals New Insight into Russeting of the Semi-Russeted ‘Cuiguan’ Pear Variety

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-01-20 | GSE194230 | GEO

Comparative Transcriptome Analysis Reveals Insight into Exocarp Russeting Pear Variety

Project description:Comparative Transcriptome Analysis Reveals Insight into Exocarp Russeting Pear Variety

| PRJNA798691 | ENA

An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of ‘Golden Delicious’ Apple

Project description:Apple skin russeting naturally occurs in many varieties, particularly in 'Golden Delicious' and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted and non-russeted skin of 'Golden Delicious' apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400 and MD17G1225100) involved in lignin biosynthesis are significant changes during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

2019-11-04 | GSE136842 | GEO

Apple russeting as seen through the RNA-seq lens: strong alterations in the exocarp cell wall

Project description:Russeting is a commercially important defect in apple (Malus x domestica) fruit production. Apple russeting is mainly characterized by the accumulation of suberin on the inner part of the cell wall. However, knowledge on the underlying genetic components triggering this trait remains sketchy. A bulk transcriptomic profiling was performed on the exocarps of three russeted and three waxy apple varieties using RNA sequencing. This experimental design was chosen to lower the specificities of each genotype. A qPCR validation was carried out on representative genes and additional contrasting varieties. Gene ontology enrichment revealed a repression of the lignin and cuticle biosynthesis genes in the russeted exocarps, concomitantly with an enhanced expression of suberin deposition, stress responsive, primary sensing, NAC and MYB-family transcription factors, and specific triterpene biosynthetic genes. Notably, a strong correlation (R2=0.976) between the expression of a MYB93-like transcription factor and key suberin biosynthetic genes was found. Our results suggest that russeting is induced by a decreased expression of the cuticle layer biosynthetic genes, leading to a stress response which not only affects suberin deposition, but also the entire structure of the cell wall. In addition, the large number of candidate genes highlighted in this study provides a solid platform for further functional investigations. In order to draw a consistent picture of the gene expression profiles specific to both russeted and waxy apples and at the same time to highlight and interpret the mechanism leading to the russeted phenotype, a bulk RNA-sequencing was performed on the exocarp of a group of three distinct fully-russeted apple varieties ('Patte de loup', 'Reinette Parmentier', 'St Edmund's Pippin') and a second one including 3 fully waxy varieties ('Gala', 'CRAW/Ma/AF42', and 'CRAW/Ma/AG94').

2015-02-01 | E-GEOD-61040 | biostudies-arrayexpress

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