Genome-wide transcriptome profiling of Gossypium spp. roots during early growth after infection with Rotylenchulus reniformis

Plant-nematode interactions have been studied extensively. The identification of genes expressed in root organs subsequent to nematode infection have been studied to a lower extent. Fewer still, potential resistance genes have been identified in cotton towards Rotylenchulus reniformis the reniform nematode (RN). Currently, there have been three cotton genomes completely sequenced. Gossypium, or cotton, genomes sequenced include: Gossypium hirsutum cv TM1, Gossypium arboreum, and Gossypium raimondii. This study imparts knowledge of differentially expressed genes (DEGs) after individual domesticated and wild cotton plants have been infected with approximately 50,000 juvenile RNs. After extraction of Total RNA from infected roots and subsequent next generation 454 pyrosequencing methods were employed, FastQC quality control measures were completed prior to Trimomatic-0.32 trimming from 33,788 reads, resulting in a significant decrease in the number of input reads (3454 input reads or DEGs). Putative descriptions were made for 634 input reads or DEGs, many of which were repeated multiple times as predicted proteins/enzymes or partials. The definition of 52 DEGs were made and enriched through the assignment of gene ontology (GO) terms that highlight categories of host plant genes for potential targets in future downstream transformation of cotton plants, especially those involved in strengthening systemic acquired resistance (SAR) or the hypersensitive response (HR) that occurs most often in plants when in defense against pathogen attack. This study reveals known protein/enzymes (52), unknown protein/enzymes (582) and unassigned DEGs (2820).