| Maize is one of the most important crop sources of food,feed and energy in the world and also the most extensively grown cereal crop in China.Sugarcane mosaic virus(SCMV)is the main pathogen of maize dwarf mosaic disease in northern China and frequently causes dramatic losses in maize production.Until now,there are some researches carried out on the transcriptional and protein levels.As another important step of gene expression,researches in the translation have relatively lagged behind because of technical limitation.Here,we established ribosome profiling system in maize which can be applied to analyze the genome-wide translational regulation.Based on ribosome profiling,we firstly analyzed the translational regulation in healthy maize,SCMV-infected and drought-stressed maize on a genome-wide scale.With both ribosome profiling and RNA-seq technologies,this research firstly systemically analyzed genome-wide translational regulation in maize.We found a widespread of translational regulation in maize seedlings.The genes with different translational efficiencies turn to have different lengths,GC contents and normalized minimal free energies in sequence.With ribosome profiling data,we detected 3,063 upstream open reading frames(uORFs)among 2,558 genes translated in maize seedlings.The translation of these uORFs significantly repressed the expression of the downstream main ORFs.We divided the infection process into 6 stages after SCMV inoculation according to symptom development on systemically infected leaves.To uncover maize translational response to SCMV infection,we collected both mock-inoculated and symptomatic leaves caused by SCMV and generated respective ribosome profiling data.The results showed that more than 2.5%ribosome protected reads(RPFs)were from SCMV genome and nearly all of which produced from positive strand of SCMV genome.About 99.7%of SCMV RPF was observed in the coding region of genomic RNA which was higher than the proportion in maize(97.5%).To reveal the influence of SCMV infection on maize gene translation,we analyzed the differential expressed gene between control(mock-inoculated)and virus-infected samples.We found that genes involved in photosynthesis pathway including those in light reaction and in Calvin cycle were downregulated at the translational level.The expression of disease resistance related genes in maize present a complicate variation in this infection stage.Genes in the pathways of gene silencing,superoxide dismutases,calcium signal transduction and protease inhibition of pathogenesis-related protein seems to be involved in the defense response against SCMV in maize.Drought is one of the major abiotic stresses maize encountered with in nature.In this research,we compared responses in transcriptional and translational levels based on RNA-seq and ribosome profiling data which generated from maize seedlings growing under normal and drought conditions,respectively.The data showed that the fold changes of gene expression at transcriptional level were correlated with those of translational level globally(R2=0.69).Nevertheless,more than half of the responsive genes were discordantly regulated at these two levels.Further analysis revealed that gene's sequence features were correlated with their responsive patterns under drought stress.Ribosome profiling method in maize was first developped in this research which provided a new tool for translational regulation analysis.Based on ribosome profiling,maize genome-wide translationall regulation was revealed,and the influence of SCMV infection and drought treatment was systemically analyzed at translational level.These results laid the foundation for understanding the molecular meachnisms of stress responses in plant. |
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