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PROVIDER: PRJNA548136 | ENA |
REPOSITORIES: ENA
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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:Plant response to insect feeding appears to be highly specific with regard to the organisms in the system. Here, we report on the interaction between grapevine Vitis vinifera plants and a phloem-feeding insect pest, the vine mealybug Planococcus ficus. Plants were exposed to P. ficus for periods of 6 hours and 96 hours, after which they were analysed for gene expression levels using microarrays and quantitative real-time PCR (qPCR). Both methods showed that grapevine displayed only a minimal response to mealybug feeding at the transcript level at both time periods. Intermediate grapevine exposure times (24, 48 and 72 hours) to P. ficus feeding were investigated using qPCR analysis of ten additional genes associated with known plant defense responses. Results showed that only a single gene, pathogenesis-related protein 1, was differentially expressed after 48 hours of mealybug feeding. During the course of mealybug feeding, however, a number of other genes were significantly up- or down-regulated at certain time points. Thus, it appears as if grapevine responds minimally to feeding by P. ficus as well as within a very narrow time period. The relative lack of grapevine plant defense mechanisms may be a result of the feeding strategies of mealybugs. Eight samples were analysed. Two replicates each were included for each treatment (6 hour and 96 hour feeding), resulting in four samples. Two control replicates were included for each treatment (6 hour and 96 hour feeding controls), resulting in a further four samples.
2012-12-01 | E-GEOD-32343 | biostudies-arrayexpress
Project description:Plant response to insect feeding appears to be highly specific with regard to the organisms in the system. Here, we report on the interaction between grapevine Vitis vinifera plants and a phloem-feeding insect pest, the vine mealybug Planococcus ficus. Plants were exposed to P. ficus for periods of 6 hours and 96 hours, after which they were analysed for gene expression levels using microarrays and quantitative real-time PCR (qPCR). Both methods showed that grapevine displayed only a minimal response to mealybug feeding at the transcript level at both time periods. Intermediate grapevine exposure times (24, 48 and 72 hours) to P. ficus feeding were investigated using qPCR analysis of ten additional genes associated with known plant defense responses. Results showed that only a single gene, pathogenesis-related protein 1, was differentially expressed after 48 hours of mealybug feeding. During the course of mealybug feeding, however, a number of other genes were significantly up- or down-regulated at certain time points. Thus, it appears as if grapevine responds minimally to feeding by P. ficus as well as within a very narrow time period. The relative lack of grapevine plant defense mechanisms may be a result of the feeding strategies of mealybugs.
2012-12-01 | GSE32343 | GEO
Project description:To uncover a suit of genes related to the consumer preferred flavours, whole RNA sequencing followed by de novo genome assembly was performed on extreme flavoured papaya varieties RB1 (preferred with sweet flavour and floral aroma) and 1B (non-preferred with bitter flavour and musty aroma) fruits at ripe and unripe stages. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different papaya varieties at ripe and unripe stages.
2022-09-19 | GSE213436 | GEO
Project description:The aim of this research was to study the effects of cis-element differences between the X, Y and Yh alleles on the expression of CpMDAR4, a potential candidate gene for sex differentiation in papaya, using a transcriptional reporter system in a model species Arabidopsis thaliana. Possible effects of a retrotransposon insertion in the Y and Yh alleles on the transcription and expression of CpMDAR4 alleles in papaya flowers were also examined. When comparing promoters and cis-regulatory elements among genes in the non-recombining region of the sex chromosomes, paired genes exhibited differences. Our results showed that differences in the promoter sequences of the CpMDAR4 alleles drove the expression of a reporter gene to different flower tissues in Arabidopsis. β-glucuronidase staining analysis of T2 and T3 lines for constructs containing 5’ deletions of native Y and Yh allele promoters showed the loss of specific expression of the reporter gene in the anthers, confirming the existence and location of cis-regulatory element POLLEN1LELAT52. The expression analysis of CpMDAR4 alleles in papaya flowers also showed that all alleles are actively expressed in different flower tissues, with the existence of a shorter truncated isoform, with unknown function, for the Y and Yh alleles due to an LTR-RT insertion in the Y and Yh chromosomes. The observed expression patterns in Arabidopsis thaliana flowers and the expression patterns of CpMDAR4 alleles in papaya flowers, suggest that MDAR4 might have a role on development of reproductive organs in papaya, and that it constitutes an important candidate for sex differentiation.
2022-07-18 | GSE208265 | GEO