Ontology highlight
ABSTRACT:
PROVIDER: PRJNA601061 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10898300.fastq.gz | Fastqsanger.gz | |||
| SRR10898301.fastq.gz | Fastqsanger.gz | |||
| SRR10898302.fastq.gz | Fastqsanger.gz | |||
| SRR10898302_1.fastq.gz | Fastqsanger.gz | |||
| SRR10898302_2.fastq.gz | Fastqsanger.gz |
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Project description:Hairy vetch (Vicia villosa Roth) is recognized as a beneficial winter cover crop in the Midwestern U.S. DNA microarrays are used for assessing gene expression significance. The objective of the study was to identify a set of genes expressed in hairy vetch, that could be further analyzed for their potential in improving the crop. The RNA of four targets (soybean (Glycine max), hairy vetch, Vicia pannonica PI 170008, and Vicia pannonica PI 515988) were purified, labeled, and hybridized to 142 cDNA clones of biotic stress genes and gene sequences of soybean that were robotically spotted onto aminosilicated slides with duplicate spots and three arrays per slide. The microarray experiments were completed in a reference design experiment incorporating a two-dye system. The data were analyzed using the individual fluorescence intensities to fit two statistical models in a mixed model analysis of variance. In this analysis, systematic error effects were observed to account for 24% of the total variation. The use of a Bonferroni adjusted significance threshold allowed for adequate control over the number of falsely identified significant genes showing expression in the different target comparisons. We observed that 64 of the 142 gene sequences (45%) were differentially expressed in at least one of the target comparisons. Two of these expressed genes in hairy vetch encoded for a cold tolerance indicator, proline, and two other gene sequences encode for stress tolerance indicators, myo-inositol and calmodulin. A soybean cDNA microarray was used effectively to differentiate gene expression in hairy vetch. Keywords: comparative genomic hybridization (cross-species)
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Project description:Background: Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center. Methodology/Principal Findings: We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula. Conclusions/Significance: Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae.
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2013-03-26 | E-GEOD-35437 | biostudies-arrayexpress