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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...

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Autores principales: Rajkumar, Hemalatha, Ramagoni, Ramesh Kumar, Anchoju, Vijayendra Chary, Vankudavath, Raju Naik, Syed, Arshi Uz Zaman
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564285/
https://www.ncbi.nlm.nih.gov/pubmed/26284934
http://dx.doi.org/10.1371/journal.pone.0135387
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author Rajkumar, Hemalatha
Ramagoni, Ramesh Kumar
Anchoju, Vijayendra Chary
Vankudavath, Raju Naik
Syed, Arshi Uz Zaman
author_facet Rajkumar, Hemalatha
Ramagoni, Ramesh Kumar
Anchoju, Vijayendra Chary
Vankudavath, Raju Naik
Syed, Arshi Uz Zaman
author_sort Rajkumar, Hemalatha
collection PubMed
description 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.
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spelling pubmed-45642852015-09-25 De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes Rajkumar, Hemalatha Ramagoni, Ramesh Kumar Anchoju, Vijayendra Chary Vankudavath, Raju Naik Syed, Arshi Uz Zaman PLoS One Research Article 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. Public Library of Science 2015-08-18 /pmc/articles/PMC4564285/ /pubmed/26284934 http://dx.doi.org/10.1371/journal.pone.0135387 Text en © 2015 Rajkumar et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Rajkumar, Hemalatha
Ramagoni, Ramesh Kumar
Anchoju, Vijayendra Chary
Vankudavath, Raju Naik
Syed, Arshi Uz Zaman
De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes
title De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes
title_full De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes
title_fullStr De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes
title_full_unstemmed De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes
title_short De Novo Transcriptome Analysis of Allium cepa L. (Onion) Bulb to Identify Allergens and Epitopes
title_sort de novo transcriptome analysis of allium cepa l. (onion) bulb to identify allergens and epitopes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564285/
https://www.ncbi.nlm.nih.gov/pubmed/26284934
http://dx.doi.org/10.1371/journal.pone.0135387
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