Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1263419 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33589419_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR33589420_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR33589421_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR33589422_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR33589423_subreads.fastq.gz | Fastqsanger.gz |
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Project description:Background: Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during fruit ripening and its control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. Results: Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes and some of them had their expression validated by qPCR. The transcription profile was then compared with that from ripening tomato and grape. Overall, the transcriptomics analysis revealed many similarities between ripening in papaya and tomato especially with respect to primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicate that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families are involved in the control of papaya ripening and reveal that cell wall-related gene expression in papaya showed similarities to the expression profiles seen in A. thaliana during hypocotyl development. Conclusion: The cross-species array experiment was successful in identifying ripening-related genes in papaya. The data indicated common and diverse elements of transcription control between fruit bearing taxa and has also indicated a possible distinct co-evolutionary mechanism for papaya cell wall disassembling system. The present study represents new topics for future researches that would help complement the structural genomic data provided by the papaya genome, since there is no gene-chip available for this plant organism. Papaya ripe transcriptome was analysed using mRNA extracted from unripe and ripe fruit from 2 replicates. After microarray hybridization in ATH1-121501 chip, data were normalized against data generated by papaya DNA hybridization in another ATH1-121501 chip and analysed using perl algorithms (masks).
2012-05-24 | E-GEOD-38105 | biostudies-arrayexpress
Project description:Background: Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during fruit ripening and its control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana. Results: Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes and some of them had their expression validated by qPCR. The transcription profile was then compared with that from ripening tomato and grape. Overall, the transcriptomics analysis revealed many similarities between ripening in papaya and tomato especially with respect to primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicate that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families are involved in the control of papaya ripening and reveal that cell wall-related gene expression in papaya showed similarities to the expression profiles seen in A. thaliana during hypocotyl development. Conclusion: The cross-species array experiment was successful in identifying ripening-related genes in papaya. The data indicated common and diverse elements of transcription control between fruit bearing taxa and has also indicated a possible distinct co-evolutionary mechanism for papaya cell wall disassembling system. The present study represents new topics for future researches that would help complement the structural genomic data provided by the papaya genome, since there is no gene-chip available for this plant organism.
2012-05-25 | GSE38105 | GEO
Project description:For identifying genes for sex determination in papaya, digital gene expression analysis by Ht-SuperSAGE (Matsumura et al., 2010) was carried out in flowers from male, female and hermaphrodite plants of papaya. Total more than 9,273,744 26bp-tags were obtained by sequence analysis using SOLiD3 and mapped on papaya primitive sex chromosome sequences.
2012-07-16 | GSE30366 | GEO
Project description:For identifying genes for sex determination in papaya, digital gene expression analysis by Ht-SuperSAGE (Matsumura et al., 2010) was carried out in flowers from male, female and hermaphrodite plants of papaya. Total more than 9,273,744 26bp-tags were obtained by sequence analysis using SOLiD3 and mapped on papaya primitive sex chromosome sequences. 6 samples examined: male young flowerbud, male mature flower bud, female young flower bud, female mature flower bud, hermaphrodite young flower bud, hermaphrodite mature flower bud
2012-07-15 | E-GEOD-30366 | biostudies-arrayexpress
Project description:The Babaco Mosaic Virus (BabMV) is a Potexvirus that affects babaco (Vasconcellea heilbornii) and papaya (Carica papaya) plants. To understand the impact of the virus on the plant, we performed a genome-wide transcriptome analysis of the response of young leaves of 3-4 months old papaya plants at 2, 10, 15- and 30-days post infection (dpi) in comparison to uninfected controls. Results showed that in mock-infected plants and virus-infected plants at 2 and 10dpi more than 90% of the reads mapped to the papaya genome. In contrast, at 15 and 30 dpi only 31% mapped to the papaya genome in BabMV infected leaves, while the remaining 69% of the reads aligned to the virus genome, demonstrating a high viral load. A total of 1585 papaya genes were differentially expressed between mock and BabMV inoculated leaves, among which cell wall biogenesis, redox signaling, and ribosome Gene Ontology terms were overrepresented, interestingly, the virus induced specific responses at different time points. Sugar metabolism and cell wall modification including lignin accumulation genes were affected at 15 dpi. At 30 days post-infection, the virus primarily induced ROS production, possibly through the activation of cytochrome P450 enzymes. This led to the upregulation of genes associated with ROS scavenging and of transcription factors (TFs) belonging to the WRKY and AP2/ERF families, which play crucial roles in activating the plant's defense mechanisms against viral pathogens. This research enhances our understanding of BabMV infections, facilitating the development of effective disease control measures.
2025-05-30 | GSE266643 | GEO
Project description:Papaya shoot tissue endophytic microbiome analysis
| PRJNA450009 | ENA
Project description:Evolving resistance to artemisinin-based compounds in SE Asia threatens to derail attempts to control and eliminate malaria. Resistance has been confirmed in western Cambodia, has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CR) from the blood following treatment. We used a two-phase approach to identify the genes underlying this ongoing selective event. Comparison of geographical differentiation and haplotype structure at 6,969 polymorphic SNPs in 91 parasites from western Cambodia, western Thailand and Laos identified 33 strongly selected genome regions. We screened SNPs and microsatellites within these genome regions in 718 parasites from western Thailand, and identified a 35kb region of chr 13 showing strong association (P=10-6 to 10-11) with slow CR. This region contains several compelling candidate loci, such as HSP70, for assessment by transfection. These results illustrate the efficacy of targeted association for identifying the genetic basis of adaptive traits.
2012-05-01 | GSE33002 | GEO