Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa.
Next-generation sequencing has transformed the ability to link genotypes to phenotypes and facilitates the dissection of genetic contribution to complex traits. However, it is challenging to link genetic variants with the perturbed functional effects on proteins encoded by such genes. Here we show how RNA sequencing can be exploited to construct genotype-specific protein sequence databases to assess natural variation in proteins, providing information about the molecular toolbox driving cellular processes. For this study, we used two natural genotypes selected from a recent genome-wide association study of Populus trichocarpa, an obligate outcrosser with tremendous phenotypic variation across the natural population. This strategy allowed us to comprehensively catalogue proteins containing single amino acid polymorphisms (SAAPs), as well as insertions and deletions. We profiled the frequency of 128 types of naturally occurring amino acid substitutions, including both expected (neutral) and unexpected (non-neutral) SAAPs, with a subset occurring in regions of the genome having strong polymorphism patterns consistent with recent positive and/or divergent selection. By zeroing in on the molecular signatures of these important regions that might have previously been uncharacterized, we now provide a high-resolution molecular inventory that should improve accessibility and subsequent identification of natural protein variants in future genotype-to-phenotype studies.
Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
Paul E
PE
Abraham
Department of Biomedical Informatics, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States.
Xiaojing
X
Wang
Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
Priya
P
Ranjan
Biological Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
Intawat
I
Nookaew
Department of Biomedical Informatics, Vanderbilt University School of Medicine , Nashville, Tennessee 37232, United States.
Bing
B
Zhang
Biological Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
Gerald A
GA
Tuskan
Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
Robert L
RL
Hettich
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D030562:Databases, Protein; D004171:Diploidy; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism*; D032107:Populus / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D017386:Sequence Homology, Amino Acid; D053719:Tandem Mass Spectrometry
D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant
RNA sequencing; genotype-specific protein database; mass spectrometry; natural variants; shotgun proteomics