Identification of circRNA in Citrus sinensis Based on Random Forest Model and Preliminary Functional Analysis
To identify circular RNA(circRNA)in Citrus sinensis genome and analyze their biological functions in the process of inter-action between C.sinensis and pathogen,a procedure for identification of circRNA was developed in python environment based on the machine learning random forest model.After comparison of different machine learning models,identification of circRNA in C.sinensis,construction of interaction network of circRNA-miRNA and circRNA-miRNA-mRNA,and gene functional enrichment analysis of circRNA-related mRNA,our results indicated that best performance was observed using random forest model compared with decision tree and feedforward neural network models.A total of 2 523 circRNA were identified in C.sinensis and they distributed unevenly on the nine chromosomes of C.sinensis as the chromosome 5 containing the maximum number with 416 circRNA.606 circRNA-miRNA and 21 043 miRNA-mRNA interaction pairs were predicted and the gene function of targeted mRNA involved in metabolism,transport and development process including phenylpropanoid biosynthesis,linoleic acid metabolism and plant-pathogen interaction.The tran-scriptional regulations of disease related miRNA like Csi-miR172 and Csi-miR482 were influenced by circRNA in C.sinensis.This study provided clues for identification and analysis of circRNA involvement in disease resistance biological process in C.sinensis.
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