Assembly, Annotation, and Proteogenomic Mapping of Rotylenchulus reniformis
Sanders, W. S., Ganji, S., Arnold, J. P., Arick, M., II, Showmaker, K. C., Bartlett, B. D., Cooksey, A., Watts, J., Knudstrup, S., Magbanua, Z. V., Peterson, D. G., & Wubben, M. J. (2014). Assembly, Annotation, and Proteogenomic Mapping of Rotylenchulus reniformis. Plant and Animal Genome XXII. San Diego, CA.
Rotylenchulus reniformis (reniform nematode) is a plant-parasitic nematode that infects a number of agriculturally important crops including cotton where it accounts for losses estimated at $130,000,000 annually. Little molecular characterization of R. reniformis has been conducted to this point. We have constructed a set of genomic sequences for R. reniformis by isolating and sequencing the genomic DNA from a pooled population of R. reniformis nematodes and assembling and annotating these sequences. In addition, we isolated proteins from R. reniformis eggs, subjected them to high-throughput liquid chromatography mass spectrometry, and searched the resulting peptide spectra against four databases – specifically, (i) the Caenorhabditis elegans proteome, (ii) the predicted proteome of Meloidogyne incognita, (iii) available R. reniformis expressed sequence tags translated in all 6 reading frames, and (iv) our assembled R. reniformis genomic sequences translated in all 6 reading frames. The resulting spectra identified 569 proteins from the three publicly available databases, while providing confirmation of 179 of our assembled genomic sequences when searched against the database of R. reniformis genomic sequences. For poorly characterized non-model organisms, comparative proteomic analysis is a powerful tool that can be utilized to quickly gain insight into the molecular infrastructure of the organism. In R. reniformis, we have shown the expression of a number of parasitism genes or gene targets as early as the egg stage and have provided confirmation that these genes are translated into proteins. Such parasitism genes/proteins may serve as targets for future applied research aimed at limiting crop damage caused by R. reniformis.