Identification And Characterization Of Non-Coding RNAs In Sogatella Furcifera

Sorgatela furcifera,Laodelphax striatellus and Nilaparvata lugens are important migratory rice pests in China and are also distributed in other countries in Southeast Asia.Sorgatela furcifera,also known as White-backed planthoppers(WBPH),directly feed on the phloem sap of rice through sucking,which not only damages the crops but also transmits plant viruses such as southern rice black-streaked dwarf virus(SRBSDV)in a persistent-propagative manner.To facilitate studies of WBPH-SRBSDV interaction mechanisms,our laboratory completed the sequencing and annotation of the white-backed planthopper genome in 2016.Taking advantage of the genomic and transcriptomic sequences,the non-coding RNAs of WBPH have been systematically characterized,and the genomic characteristics,evolutionary conservation and possible action mechanisms of these non-coding RNAs(ncRNAs)were investigated in the dissertation.Three classes of small RNAs have been defined,including microRNAs(miRNAs),siRNAs and Piwi-interacting RNAs(piRNAs).Research has indicated that small RNAs play important roles in gene regulation and antiviral mechanism in invertebrate.In this study,554 miRNAs including 107 conserved miRNAs and 447 novel miRNAs were identified in WBPH by analyzing small RNA libraries of WBPH cells and adults.Compared with miRNAs of 26 insects and 5 non-insect species deposited in miRBase,we found that more than half miRNAs of the conserved families in WBPH were highly conserved across all insects,while other conserved miRNA families were conserved in non-dipteran insects.We also found that some conserved miRNA precursors of WBPH generate dominant mature miRNAs from the opposite arms in Drosophila melanogaster and Tribolium castaneum.We also characterized the sex-biased miRNAs in WBPH.Moreover,8 up-and 4 down-regulated miRNAs were identified in WBPH cells in response to SRBSDV infection,in which miR-14 and miR-n98a were supposed to be involved in the immune response.We also characterized the siRNA and piRNA clusters in WBPH genome by analyzing 6 small RNA libraries of WBPH adults.Using the bioinformatic pipelines developed in the study,149 siRNA clusters and 108 piRNA clusters were identified in WBPH genome.Most(53%)of the piRNAs were derived from type I transposons,including 26%of long interspersed nuclear elements,21%of Long terminal repeats and 2%of short interspersed nuclear elements.In contrast,32%and 66%of all transposon-derived endogenous siRNAs were derived from retrotransposons and DNA transposons,respectively.These results suggested that piRNAs and siRNAs regulates the activities of different classes of transposons.Sex-biased piRNA clusters and siRNA clusters were also observed in WBPH,including 15 piRNA clusters and 10 siRNA clusters with higher expression levels in female and 5 piRNA clusters and 7 siRNA clusters in male.Of note,both siRNA and piRNA clusters were identified in ATP1B2 gene locus,and the expression level of ATP1B2 gene was negatively correlated to the expression levels of these siRNAs and piRNAs.Long non-coding RNAs(IncRNAs)are a class of important ncRNAs larger than 200 nt in length.Circular RNAs(circRNA)are another class of ncRNA generated by back-splicing.circRNAs have no 5’ cap and 3’ polyA tail.LncRNA and circRNA play important roles in gene transcription,epigenetic regulation and diseases.We analyzed 8 RNA-seq libraries derived from different developmental stages of WBPH and identified 1861 IncRNA transcripts from 1852 loci in WBPH genome.We found that IncRNAs have higher developmental-stage expression specificity than protein-coding genes.In embryos,4th and 5th instars,there are more up-regulated IncRNAs identified in embryos,4th and 5th instars of WBPH,suggesting that these IncRNAs may play roles in these development stages.We also investigated the expressional correlations between IncRNAs and their adjacent protein-coding genes and found higher correlation between IncRNAs and the adjacent downstream protein-coding genes located on the antisense strand.We also identified 390 IncRNA transcripts from 385 loci in Laodelphax striatellus(small brown planthopper,SBPH)genome by analyzing 3 RNA-seq datasets.We also identified 93 and 49 conserved IncRNAs in WBPH and SBPH,respectively.Furthermore,we identified 1706 circRNAs in WBPH genome using CIRCexplorer and investigated the expressional profiles of these circRNAs at different developmental stages.Moreover,3 female-biased and 12 male-biased circRNAs were identified,and the host genes of male-biased circRNAs are associated with neural development and gender development.In conclusion,this paper developed a variety of bioinformatics analysis processes for WBPH ncRNA identification based on the genomic information of the WBPH,combined with small RNA and RNA-seq high-throughput sequencing data from different sources of WBPH.We systematically identified the miRNA,siRNA cluster,piRNA cluster,IncRNA and circRNA of the WBPH,and studied the genomic characteristics,evolutionary conservation and possible mechanism of action of these ncRNAs.These findings provide a solid basis for further study of the molecular mechanisms of action of these ncRNAs.