Working group session:
Comparative Genomics and Bioinformatics
Presentation type:
poster
Authors:
Li, Ruijuan; Hu, Hongtao; Weaver, David; Lawrence, Kathy; Singh, Narendra; Locy, Robert
Presenter:
Li, Ruijuan
Correspondent:
Hu, Hongtao; Locy, Robert
Abstract:
Reniform nematodes (RN, Rotylenchlus reniformis) are semi-endoparasitic nematode species causing significant yield loss in cotton. In response to parasitic nematode infestation, plants demonstrate susceptible, resistant, and/or hypersensitive responses. The nature of the plant response relies on the coordination of different resistance mechanisms including specific resistance genes or proteins, several plant hormone pathways, reactive oxygen species (ROS), and pathogenesis related effector proteins. These resistance-related elements and signaling pathways crosstalk to each other and can be seen as an integrated signaling network mediated by transcription factors and small regulatory RNAs (sRNAs) at the transcriptional (epigenetic), posttranscriptional, and/or translational levels. The objective of this study is to identify and characterize such regulatory networks in cotton genotypes that are susceptible, resistant, and hypersensitive to RN infestation. To accomplish this objective, six sRNA and six cDNA libraries were constructed from RN susceptible cotton genotypes (DP90 and SG747 combined as one sample), resistant genotype (BARBREN-713), and hypersensitive genotype (LONREN-1) with or without RN infestation. The sRNA and cDNA libraries were submitted for deep sequencing using the Illumina platform generating 6 corresponding datasets. Various classes of sRNAs were identified in the sRNA datasets using an sRNA bioinformatics pipeline, including microRNAs (miRNAs) and other hairpin sRNAs, repeat associated small interfering RNAs (ra-siRNAs), phased and nonphased secondary siRNAs, and cis- and trans-natural antisense small interfering RNAs. Among them, 28 conserved and 24 novel miRNAs exhibited statistically significant differential expression in response to RN infestation, and over 90% of these RN responsive miRNAs were distinctly regulated in different genotypes. The spectrum of miRNAs target genes include both expected and novel genes previously implicated in plant innate immunity, hormone signaling, ROS generation and related signaling. In addition, RN responsive miR482 initiated secondary siRNAs were distinctly accumulated in response to RN infestation in cotton susceptible, resistance, and hypersensitive genotypes. Notably, NBS-LRR protein coding genes are the targets of miR482, which generate secondary siRNAs. This type of sRNA regulatory network has been implicated in plant innate immunity to a variety of pathogens, and thus, we have produced insights into the specific aspects of this network regulated during RN infestation of cotton roots. For cDNA sequencing, over 150 million raw reads were generated from Illumina sequening platform using the 6 cDNA libraries above. These reads were trimmed and cleaned and de novo assembled into putative transcripts that ranged from 200 bp to greater than 5000 bp. Gene expression and biological function analysis has been used to to determination up and down regulated RN responsive genes. Expression of genes that are targets of RN responsive sRNA and/or are involved in sRNA regulatory networks will be compared to the predicted results from regulatory networks to determine cotton the molecular basis of susceptible, resistant, and hypersensitive responses.