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

Biology

Yoko Adachi¹  Timothy R. Croley²  Cary Pirone-Davies²  Melinda A. McFarland²  Christine H. Parker² 

[1] Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA;Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA;

关键词: nut allergen;    walnut;    pecan;    Juglans regia;    de-novo transcriptome;    proteomics;   

DOI  :  10.3390/biology9050104

来源: DOAJ

【 摘 要 】

As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with Juglans regia, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography–mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156–1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms.

【 授权许可】

Unknown