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RNA-Seq Analysis of Developing Pecan (Carya illinoinensis) Embryos Reveals Parallel Expression Patterns among Allergen and Lipid Metabolism Genes
- Source :
- Journal of agricultural and food chemistry. 65(7)
- Publication Year :
- 2017
-
Abstract
- The pecan nut is a nutrient-rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. The transcriptome of a developing pecan nut was characterized to identify the gene expression occurring during the process of nut development and to highlight those genes involved in fatty acid metabolism and those that commonly act as food allergens. Pecan samples were collected at several time points during the embryo development process including the water, gel, dough, and mature nut stages. Library preparation and sequencing were performed using Illumina-based mRNA HiSeq with RNA from four time points during the growing season during August and September 2012. Sequence analysis with Trinotate software following the Trinity protocol identified 133,000 unigenes with 52,267 named transcripts and 45,882 annotated genes. A total of 27,312 genes were defined by GO annotation. Gene expression clustering analysis identified 12 different gene expression profiles, each containing a number of genes. Three pecan seed storage proteins that commonly act as allergens, Car i 1, Car i 2, and Car i 4, were significantly up-regulated during the time course. Up-regulated fatty acid metabolism genes that were identified included acyl-[ACP] desaturase and omega-6 desaturase genes involved in oleic and linoleic acid metabolism. Notably, a few of the up-regulated acyl-[ACP] desaturase and omega-6 desaturase genes that were identified have expression patterns similar to the allergen genes based upon gene expression clustering and qPCR analysis. These findings suggest the possibility of coordinated accumulation of lipids and allergens during pecan nut embryogenesis.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Sequence analysis
RNA-Seq
Biology
01 natural sciences
Transcriptome
03 medical and health sciences
chemistry.chemical_compound
food
Gene expression
Gene
Carya
chemistry.chemical_classification
Fatty acid metabolism
food and beverages
Fatty acid
Carya illinoinensis
General Chemistry
Allergens
Lipid Metabolism
food.food
030104 developmental biology
Biochemistry
chemistry
RNA, Plant
Seeds
Seasons
General Agricultural and Biological Sciences
010606 plant biology & botany
Subjects
Details
- ISSN :
- 15205118
- Volume :
- 65
- Issue :
- 7
- Database :
- OpenAIRE
- Journal :
- Journal of agricultural and food chemistry
- Accession number :
- edsair.doi.dedup.....1bbaa9a21c73db75ed0c82daf7100044