Identification of Protein Coding Genes in the Plant-parasitic Nematode Rotylenchulus reniformis through Comparative Proteogenomic Mapping with Caenorhabditis elegans

Sanders, W. S., Ganji, S., Arnold, J. P., Arick, M., II, Showmaker, K. C., Wubben, M. J., & Peterson, D. G. (2013). Identification of Protein Coding Genes in the Plant-parasitic Nematode Rotylenchulus reniformis through Comparative Proteogenomic Mapping with Caenorhabditis elegans. MCBIOS 2013. University of Missouri, Columbia, MO.

Peptides identified through high-throughput mass spectrometry can be utilized to complement traditional structural genome annotation methods through proteogenomic mapping and provide experimental evidence that a given gene is being transcribed and translated into a protein. In model organisms, proteogenomic mapping can aid researchers by identifying novel exons and aid in the identification of intron-exon boundary correction and discovery. In non-model organisms, the peptides identified through mass spectrometry can be mapped back to the genome sequence of a model organism, providing insight into genes conserved in the non-model species. Rotylenchulus reniformis is a plant parasitic nematode affecting US cotton production, and causes an estimated annual $130,000,000 USD crop loss. Proteins were isolated from R. reniformis eggs and subjected to proteolytic digestion and analysis through mass spectrometry. Genomic R. reniformis DNA was isolated and sequences were generated using two platforms, combining both Illumina Sequencing-by-Synthesis and Roche 454 Pyrosequencing technologies. Through the proteogenomic mapping of these peptides to the proteome and genome of the model nematode species, Caenorhabditis elegans, and the use of the R. reniformis genome sequence data, we have identified a set of gene sequences to serve as a validation set for our ongoing efforts to sequence and assembly the genome of Rotylenchulus reniformis.