title: RNA-Seq Analysis of Developing Pecan (Carya illinoinensis) Embryos Reveals Parallel Expression Patterns among Allergen and Lipid Metabolism Genes.
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.
authors.affiliation: Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture , 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, United States.
authors.forename: Christopher P
authors.identifier: http://orcid.org/0000-0001-7819-0914
authors.initials: CP
authors.lastname: Mattison
authors.affiliation: Virginia Bioinformatics Institute , 1015 Life Science Circle, Blacksburg, Virginia 24061, United States.
authors.forename: Ruhi
authors.initials: R
authors.lastname: Rai
authors.affiliation: Virginia Bioinformatics Institute , 1015 Life Science Circle, Blacksburg, Virginia 24061, United States.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Settlage
authors.affiliation: Southern Regional Research Center, CCU, ARS, U.S. Department of Agriculture , 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, United States.
authors.forename: Doug J
authors.initials: DJ
authors.lastname: Hinchliffe
authors.affiliation: Southern Regional Research Center, CCU, ARS, U.S. Department of Agriculture , 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, United States.
authors.forename: Crista
authors.initials: C
authors.lastname: Madison
authors.affiliation: Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture , 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, United States.
authors.forename: John M
authors.initials: JM
authors.lastname: Bland
authors.affiliation: Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture , 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, United States.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Brashear
authors.affiliation: Pecan Research & Extension Station, Agricultural Experiment Station, Louisiana State University-AgCenter , 10300 Harts Island Road, Shreveport, Louisiana 71115, United States.
authors.forename: Charles J
authors.initials: CJ
authors.lastname: Graham
authors.affiliation: Biologics, Bayer CropScience , 890 Embarcadero Drive, West Sacramento, California 95605, United States.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Tarver
authors.affiliation: Southern Regional Research Center, CFB, ARS, U.S. Department of Agriculture , 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, United States.
authors.forename: Christopher
authors.initials: C
authors.lastname: Florane
authors.affiliation: Southern Regional Research Center, FPSQ, ARS, U.S. Department of Agriculture , 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, United States.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bechtel
mesh_terms: D000485:Allergens / Q000235:genetics* / Q000378:metabolism; D031325:Carya / Q000196:embryology* / Q000235:genetics* / Q000378:metabolism; D050356:Lipid Metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D012621:Seasons; D012639:Seeds / Q000201:enzymology / Q000235:genetics / Q000378:metabolism
chemical_list: D000485:Allergens; D018749:RNA, Plant
keywords: allergy; development; fatty acid; metabolism; nut; pecan; transcriptome