Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa
Abstract
The availability of next-generation sequencing technologies has rapidly transformed our ability to link genotypes to phenotypes, and as such, promises to facilitate the dissection of genetic contribution to complex traits. Although discoveries of genetic associations will further our understanding of biology, once candidate variants have been identified, investigators are faced with the challenge of characterizing the functional effects on proteins encoded by such genes. Here we show how next-generation RNA sequencing data can be exploited to construct genotype-specific protein sequence databases, which provide a clearer picture of the molecular toolbox underlying cellular and organismal processes and their variation in a natural population. For this study, we used two individual genotypes (DENA-17-3 and VNDL-27-4) from a recent genome wide association (GWA) study of Populus trichocarpa, an obligate outcrosser that exhibits tremendous phenotypic variation across the natural population. This strategy allowed us to comprehensively catalogue proteins containing single amino acid polymorphisms (SAAPs) and insertions and deletions (INDELS). Based on large-scale identification of SAAPs, we profiled the frequency of 128 types of naturally occurring amino acid substitutions, with a subset of SAAPs occurring in regions of the genome having strong polymorphism patterns consistent with recent positive and/or divergent selection. In addition, we weremore »
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Vanderbilt Univ., Nashville, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1246772
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Proteome Research
- Additional Journal Information:
- Journal Volume: 14; Journal Issue: 12; Journal ID: ISSN 1535-3893
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; natural variants; mass spectrometry; shotgun proteomics; RNA sequencing; genotype-specific protein database
Citation Formats
Abraham, Paul E., Wang, Xiaojing, Ranjan, Priya, Zhang, Bing, Tuskan, Gerald A., Robert L. Hettich, and Nookaew, Intawat. Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa. United States: N. p., 2015.
Web. doi:10.1021/acs.jproteome.5b00823.
Abraham, Paul E., Wang, Xiaojing, Ranjan, Priya, Zhang, Bing, Tuskan, Gerald A., Robert L. Hettich, & Nookaew, Intawat. Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa. United States. https://doi.org/10.1021/acs.jproteome.5b00823
Abraham, Paul E., Wang, Xiaojing, Ranjan, Priya, Zhang, Bing, Tuskan, Gerald A., Robert L. Hettich, and Nookaew, Intawat. Tue .
"Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa". United States. https://doi.org/10.1021/acs.jproteome.5b00823. https://www.osti.gov/servlets/purl/1246772.
@article{osti_1246772,
title = {Integrating mRNA and protein sequencing enables the detection and quantitative profiling of natural protein sequence variants of Populus trichocarpa},
author = {Abraham, Paul E. and Wang, Xiaojing and Ranjan, Priya and Zhang, Bing and Tuskan, Gerald A. and Robert L. Hettich and Nookaew, Intawat},
abstractNote = {The availability of next-generation sequencing technologies has rapidly transformed our ability to link genotypes to phenotypes, and as such, promises to facilitate the dissection of genetic contribution to complex traits. Although discoveries of genetic associations will further our understanding of biology, once candidate variants have been identified, investigators are faced with the challenge of characterizing the functional effects on proteins encoded by such genes. Here we show how next-generation RNA sequencing data can be exploited to construct genotype-specific protein sequence databases, which provide a clearer picture of the molecular toolbox underlying cellular and organismal processes and their variation in a natural population. For this study, we used two individual genotypes (DENA-17-3 and VNDL-27-4) from a recent genome wide association (GWA) study of Populus trichocarpa, an obligate outcrosser that exhibits tremendous phenotypic variation across the natural population. This strategy allowed us to comprehensively catalogue proteins containing single amino acid polymorphisms (SAAPs) and insertions and deletions (INDELS). Based on large-scale identification of SAAPs, we profiled the frequency of 128 types of naturally occurring amino acid substitutions, with a subset of SAAPs occurring in regions of the genome having strong polymorphism patterns consistent with recent positive and/or divergent selection. In addition, we were able to explore the diploid landscape of Populus at the proteome-level, allowing the characterization of heterozygous variants.},
doi = {10.1021/acs.jproteome.5b00823},
journal = {Journal of Proteome Research},
number = 12,
volume = 14,
place = {United States},
year = {Tue Oct 20 00:00:00 EDT 2015},
month = {Tue Oct 20 00:00:00 EDT 2015}
}
Search WorldCat to find libraries that may hold this journalWeb of Science