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The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts
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 cons...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7284556/ https://www.ncbi.nlm.nih.gov/pubmed/32438695 http://dx.doi.org/10.3390/biology9050104 |
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author | Pirone-Davies, Cary McFarland, Melinda A. Parker, Christine H. Adachi, Yoko Croley, Timothy R. |
author_facet | Pirone-Davies, Cary McFarland, Melinda A. Parker, Christine H. Adachi, Yoko Croley, Timothy R. |
author_sort | Pirone-Davies, Cary |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7284556 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-72845562020-06-19 The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts Pirone-Davies, Cary McFarland, Melinda A. Parker, Christine H. Adachi, Yoko Croley, Timothy R. Biology (Basel) Article 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. MDPI 2020-05-19 /pmc/articles/PMC7284556/ /pubmed/32438695 http://dx.doi.org/10.3390/biology9050104 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Pirone-Davies, Cary McFarland, Melinda A. Parker, Christine H. Adachi, Yoko Croley, Timothy R. The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
title | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
title_full | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
title_fullStr | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
title_full_unstemmed | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
title_short | The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts |
title_sort | utility of genomic and transcriptomic data in the construction of proxy protein sequence databases for unsequenced tree nuts |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7284556/ https://www.ncbi.nlm.nih.gov/pubmed/32438695 http://dx.doi.org/10.3390/biology9050104 |
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