Paper

Novel allergen discovery through comprehensive de novo transcriptomic analyses of 5 shrimp species

Taki, Aya C, Huerlimann, Roger, Karnaneedi, Shaymaviswanathan, Ruethers, Thimo, Lopata, Andreas L, Johnston, Elecia B, Wade, Nicholas M, Nugraha, Roni, Jerry, Dean R, Kamath, Sandip D

2020

Overview

Shellfish allergy affects up to 2% of the world population and persists for life in most patients. The diagnosis of a shellfish allergy, in particular shrimp, is however often challenging due to the similarity of allergenic proteins in other invertebrates. Despite the clinical importance, the complete allergen repertoire of allergy-causing shrimps remains unclear. Here we mine the complete transcriptome of five frequently consumed shrimp species to identify and compare allergens with all known allergen sources. The transcriptomes were assembled de novo from raw RNA-Seq data of the whiteleg shrimp (Litopenaeus vannamei), black tiger shrimp (Penaeus monodon), banana shrimp (Fenneropenaeus merguiensis), king shrimp (Melicertus latisulcatus), and endeavour shrimp (Metapenaeus endeavouri). Trinity was used to assemble the transcriptome, and Transrate and BUSCO applied to verify the assembly. Blast search with the two major allergen databases, WHO/IUIS Allergen Nomenclature and AllergenOnline, successfully identified all seven known crustacean allergens. Salmon was utilised to measure their relative abundance, demonstrating sarcoplasmic calcium-binding protein, arginine kinase and myosin light chain as highly abundant allergens. In addition, the analyses revealed up to 40 unreported allergens in different shrimp species, including heat shock protein (HSP), alpha-tubulin, chymotrypsin, cyclophilin, beta-enolase, aldolase A, and glyceraldehyde-3-phosphate dehydrogenase (G3PD). Multiple sequence alignment, conducted in Jalview 2.1 with Clustal Omega, demonstrated high homology with allergens from other invertebrates including mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable genomic resource for investigating shellfish allergens, comparing invertebrate allergens and developing improved diagnostics and novel immunotherapeutics for food allergy. Competing Interest Statement The authors have declared no competing interest.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Allergens / Allergies / Arginine / Arginine kinase / Bioinformatics / Calcium-binding protein / Chymotrypsin / Fenneropenaeus merguiensis / Food allergies / Food sources / Gene expression / Genomics / Glyceraldehyde-3-phosphate dehydrogenase / Heat shock proteins / Homology / Invertebrates / Litopenaeus vannamei / Melicertus latisulcatus / Metapenaeus endeavouri / Myosin / Nucleotide sequence / Penaeus latisulcatus / Penaeus monodon / Phosphopyruvate hydratase / Ribonucleic acid / RNA / Shellfish / Species / Transcriptomics / Tubulin