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.

Combining independent de novo assemblies to optimize leaf transcriptome of Persian walnut

“…Of the merged assemblies, Transfuse showed a slightly better performance based on the final score of BUSCO, but it produced more than double the number of contigs generated by the other merging assembler, indicating that this tool produced more redundancy relative to EvidentialGene. Also, this finding was not in line with a few previous studies on walnut and on other close plants [11,37,41]. In this regard, the number of duplicated copies (based on BUSCO analysis) was higher in Transfuse (85.8%) than in EvidentialGene (44.1%), which can be considered as a weakness of Transfuse.…”

Isolation and Characterization of Three Chalcone Synthase Genes in Pecan (Carya illinoinensis)

“…Gene-specific primers of CiCHS1 were designed using Primer 5.0 (Table S1). Expression profiles of CiCHSs were detected using qRT-PCR on a QuantStudio 7 Flex Real-Time PCR System (Applied Biosystems) and were normalized to the 18s RNA housekeeping gene [45]. The qRT-PCR reactions were performed according to the PrimeScript RT reagent qPCR Kit manual (TaKaRa, Dalian, China).…”

The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts

“…Both analyses were implemented in R [40], and statistical significance was evaluated at alpha equal to 0.05. As a second dataset, ~310 million reads (paired-end, 100 bp) from four stages of nut development of Carya illinoinensis, pecan [41] were downloaded from the Sequence Read Archive (SRA) [42] at the National Center for Biotechnology Information (NCBI) and processed as the walnut reads. However, reads were quality trimmed to phred 30 instead of phred 35.…”