Digital transcriptome analysis of genes on sex chromosomes in papaya (Carica papaya)
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ABSTRACT:
ORGANISM(S): Carica papaya
PROVIDER: GSE30366 | GEO | 2012/07/16
SECONDARY ACCESSION(S): PRJNA143415
REPOSITORIES: GEO
Similar Datasets
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 aim of this study was to identify differentially expressed genes among male, female and hermaphrodite flowers in papaya during early (pre-meiosis) and later (post-meiosis) stages of flower development. We identified a Male Sterility 1 gene (CpMS1) highly up-regulated in male and hermaphrodite flower buds compared to female flower buds. Besides important transcription factors related to flower organ development and flowering time regulation, we identified differential expression of genes that are known to participate in ABA, ROS and auxin signaling pathways.
2019-10-25 | GSE137547 | 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
Project description:The tissues of male flowers, female flowers and hermaphrodite are collected and stored in liquid nitrigen immediately. Total RNA was isolated from male, hermaphrodite, and female flowers using the Trizol reagent (Invitrogen USA). Low molecular weight RNA was enriched from the total RNA by precipitating with 0.4M NaCl and polyethylene glycol (PEG). The enriched low molecular weight RNA was then separated on a denaturing 15% polyacrylamide gel. The band corresponding to the RNA standard of 18-30 nucleotides was then excised from the gel and eluted overnight in 0.4M NaCl at 4 degrees Celsius, and subsequently ligated with 5’ and 3’ Illumina small RNA adapters. The adapter ligated library was converted into cDNA and amplified by using PCR and sequenced by Illumina Genome Analyzer II.
2014-12-31 | GSE54097 | GEO
Project description:Digital transcriptome analysis of genes on sex chromosomes in papaya (Carica papaya)
| PRJNA143415 | ENA
Project description:Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual systems. Male and female plants of C. grandis have 22A+XY and 22A+XX chromosomes respectively. Previously, we have reported a gynomonoecious form (GyM) (22A+XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we showed that foliar spray of silver nitrate on female C. grandis plant induces development of morphologically hermaphrodite buds (Ag-H) despite the absence of Y chromosome. To identify sex-related differences, total protein from the flower buds of male, female, GyM-H and Ag-H of C. grandis at early and middle stages of development were analysed by a powerful label-free proteomics approach on ABSCIEX Triple TOF 5600 platform.
2019-07-29 | PXD011064 | Pride
Project description:Digital gene expression analysis by Ht-SuperSAGE (Matsumura et al. 2011. High-Throughput SuperSAGE. Methods Mol Biol.) was carried out to compare gene expression between wild type and mutant cell lines of the green algae Dunaliella tertiolecta under different light levels.
2020-06-30 | GSE129614 | GEO
Project description:SuperSAGE is a method of digital gene expression profiling that allows isolation of 26bp tag fragments from expressed transcripts. Because its tag size is larger than that of conventional SAGE, SuperSAGE allowed a secure tag-to-gene annotation using BLAST search against grape genome databases.Transcript profiles in nine samples of grape berry tissues under different light conditions were obtained by SuperSAGE analysis and used for screening the genes which have co-ordinated transcript profiles with the change in the flavonoid composition in the samples analyzed. Candidate genes related to flavonoid biosynthesis and regulation were identified. Nine different grape samples, i.e., flowers, grape berries of Cabernet Sauvignon at 2, 7, 9 weeks after flowering (WAF), berry skins at 17 days after flowering (DAF) shaded after flowering, and berry skins at 17DAF shaded from flowering to 14DAF and then light exposed, were analyzed.
2014-06-03 | E-GEOD-55473 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Carica papaya tissues (including leaves and flowers). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, virus-infected leaves and female flowers of Carica papaya. Total RNA was isolated using the TriReagent (Molecular Research Center) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Ray Ming and Qingyi Yu for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-04-29 | E-GEOD-28753 | 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. 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