HPC MSU

Publication Abstract

Sequencing and Analysis of the Rotylenchulus reniformis Transcriptome

Showmaker, K. C., Sanders, W. S., Bartlett, B., Wang, H, Ganji, S., Wubben, M. J., McCarthy, F.M., Magbanua, Z. V., & Peterson, D. G. (2012). Sequencing and Analysis of the Rotylenchulus reniformis Transcriptome. Plant and Animal Genome XX. San Diego, CA.

Abstract

Rotylenchulus reniformis, commonly known as the reniform nematode, is a crop pathogen of cotton, soybean, and sweet potatoes in the Southeastern United States. Compared to the resources available for other plant parasitic nematodes, such as the southern root-knot nematode, Meloidogyne incognita, and the soybean cyst nematode, Heterodera glycines, there are currently few genetic resources available to researchers studying the reniform nematode. Using resources available for both the southern root-knot nematode and the soybean cyst nematode, researchers have conducted RNAi studies to knock out specific genes, preventing those nematodes from establishing feeding sites and parasitizing their host plants. Knowledge of the reniform nematode’s transcript sequences can facilitate additional RNAi research, which can lead to a better understanding of its physiology and parasitism mechanisms. Using sequences generated from both Illumina Sequencing-by-Synthesis and Sanger EST reads, we performed a de novo transcriptome assembly for the reniform nematode. Additionally, these RNA-seq sequences have been utilized to help identify coding regions in the recently assembled reniform nematode genome. Using these RNA-seq sequences, derived from eggs and vermiform nematodes, gene expression patterns for these two life stages of the reniform nematode were also analyzed. We present the current status of our reniform nematode transcriptome sequencing, assembly, annotation, and gene expression project.