Petunia axillaris subsp. parodii
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Project description:Petunia axillaris subsp. axillaris cultivar:N Assembly
| PRJNA321982 | ENA
Project description:Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been rarely applied because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of the transcriptome of each species, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in both species. In addition, microarray analysis was applied to explore the molecular basis of the seed coat defects in Petunia hybrida mutants, homozygous for a null allele of the AN11 gene, encoding a WDR transcription regulator. Among the transcripts differentially expressed in an11 seeds compared to wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida.
2012-02-29 | GSE28120 | GEO
Project description:Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been rarely applied because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of the transcriptome of each species, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in both species. In addition, microarray analysis was applied to explore the molecular basis of the seed coat defects in Petunia hybrida mutants, homozygous for a null allele of the AN11 gene, encoding a WDR transcription regulator. Among the transcripts differentially expressed in an11 seeds compared to wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida. The manuscript describes the creation by next generation sequencing of a large catalogue of the transcriptome of the two Petunia species, that are considered to represent the natural material from which the breeders selected their varieties. This submission represents the transcriptome component of study. The high throughput sequencing data were submitted to SRA (accession numbers: SRA027293, SRP004866.1, SRX036999.2, SRX036998.2).
2012-02-29 | E-GEOD-28120 | biostudies-arrayexpress
Project description:Petunia axillaris cultivar:N Genome sequencing and assembly
| PRJNA321987 | ENA
Project description:Petunia axillaris strain:PI 667515 Transcriptome or Gene expression
| PRJNA261953 | ENA
Project description:Petunia axillaris x Petunia exserta RILs Raw sequence reads
| PRJNA704924 | ENA
Project description:We performed one degradome sequencing for identification and characterization of novel microRNAs in Phalaenopsis aphrodite subsp. formosana. Plant tissues of leaves, stalk, and flower buds frozen in liquid nitrogen were ground to fine powder using a mortar and pestle, respectively. Total RNA extraction was freshly prepared using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. About 50 μg of leaves with or without low temperature treatment, stalks and flower buds were taken separately and then mixed. The degradome library was constructed by the Genomics BioSci & Tech. Company following the manufactoring protocol. In brief, 200 μg of total RNA was passed though polyA column using the Oligotex kit (Qiagen). The 5'-RNA adapter containing a Mme I recognition site was ligated by T4 RNA ligase and further reverse transcribed to amplify the templates. After digesting with Mme I then ligated to a 3'-double DNA adapter, the products were amplified by additional PCR cycles and gel-purified for Illumina sequencing. The files contain the raw data of degradome sequencing.
2012-11-06 | GSE35739 | GEO
Project description:RNA-seq of Petunia floral buds for differences in flavonol-related genes
| PRJNA300613 | ENA