De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes.
Allium cepa (onion) is a diploid plant with one of the largest nuclear genomes among all diploids. Onion is an example of an under-researched crop which has a complex heterozygous genome. There are no allergenic proteins and genomic data available for onions. This study was conducted to establish a transcriptome catalogue of onion bulb that will enable us to study onion related genes involved in medicinal use and allergies. Transcriptome dataset generated from onion bulb using the Illumina HiSeq 2000 technology showed a total of 99,074,309 high quality raw reads (~20 Gb). Based on sequence homology onion genes were categorized into 49 different functional groups. Most of the genes however, were classified under 'unknown' in all three gene ontology categories. Of the categorized genes, 61.2% showed metabolic functions followed by cellular components such as binding, cellular processes; catalytic activity and cell part. With BLASTx top hit analysis, a total of 2,511 homologous allergenic sequences were found, which had 37-100% similarity with 46 different types of allergens existing in the database. From the 46 contigs or allergens, 521 B-cell linear epitopes were identified using BepiPred linear epitope prediction tool. This is the first comprehensive insight into the transcriptome of onion bulb tissue using the NGS technology, which can be used to map IgE epitopes and prediction of structures and functions of various proteins.
Department of Microbiology & Immunology, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, Telangana State, 500 007, India.
Hemalatha
H
Rajkumar
Department of Microbiology & Immunology, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, Telangana State, 500 007, India.
Ramesh Kumar
RK
Ramagoni
Department of Microbiology & Immunology, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, Telangana State, 500 007, India.
Vijayendra Chary
VC
Anchoju
Biomedical Informatics Center, National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, Telangana State, 500007, India.
Raju Naik
RN
Vankudavath
Nucleome Informatics Pvt. Ltd., Hyderabad, Telangana State, 500 049, India.
Arshi Uz Zaman
AU
Syed
D000485:Allergens / Q000235:genetics*; D015415:Biomarkers / Q000378:metabolism*; D000939:Epitopes / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D019697:Onions / Q000235:genetics* / Q000254:growth & development; D010940:Plant Proteins / Q000235:genetics*; D018517:Plant Roots / Q000235:genetics*
D000485:Allergens; D015415:Biomarkers; D000939:Epitopes; D010940:Plant Proteins