GSE173818
Interplay between gene expression, histone modifications, and DNA methylation mediated by miR778 during beet cyst nematode parasitism of Arabidopsis [RNA-seq]
Purpose: The aim of this study is to investigate the role of H3K9 methylation in the development of syncytia induced by the beet cyst nematode (BCN, Heterodera schachtii). For this, differential gene expression analysis was performed in root tissues of Col-0 wild-type and suvh5 and suvh6 single mutants under BCN-infected and noninfected conditions. Methods: Col-0 wild-type and suvh5 and suvh6 mutant plants were grown and 10-day-old plants were inoculated with 100 second-stage juvenile (J2) H. schachtii at 10 days old. Five days post inoculation, root tissues were collected from infected and noninfected plants in triplicate. Total RNA was extracted, mRNA libraries were prepared, and then high throughput RNA sequencing was performed using the Illumina NovoSeq 6000. High quality, paired-end reads were then aligned to the Arabidopsis thaliana reference genome (TAIR10.28) using STAR and uniquely mapped reads were counted using HTSeq. Finally, differentially expressed genes (DEGs) between the mutant lines and wild-type plants under non-infected and infected conditions were identified using DESeq package. Results and conclusions: At least 20 million reads were uniquely mapped to the Arabidopsis reference genome with an average length of about 300 bp for paired-end reads. A total of 1057 and 3390 DEGs were identified for suvh5 and suvh6 versus Col-0, respectively, under noninfected conditions. Upon infection of BCN, Col-0 had 4566 DEGs compared to the noninfected wild type. BCN-infected single mutants suvh5 and suvh6 had 2487 and 846 DEGs compared to BCN-infected Col-0, respectively. Of these DEGs, 1277 and 592 or about 51% and 70% are also differentially expressed in BCN-infected Col compared to noninfected Col-0, respectively, and 324 of the 1277 and 592 DEGs are common to BCN-infected suvh5 and suvh6 compared to the control. DEGs common to BCN-infected Col-0 and/or suvh5, and suvh6 are involved in stress and defense responses, primary and secondary metabolism, signal transduction, cell wall organization and other cellular processes. This suggests that SUVH5 and SUVH6 play a major role in transcriptome reprogramming to facilitate cellular, molecular, and metabolic processes involved in the compatible plant-nematode interaction. Overall design: Transcriptional profiles of H. schachtii infected and noninfected suvh5 and suvh6 mutants compared to Col-0 wild type