| Non-coding RNA is the RNA that can not code protein.Based on the length of non-coding RNAs,they are classified into small non-coding RNAs shorter than 50 nt,such as microRNA(miRNA),and long non-coding RNA(lncRNAs)longer than 200 nt.The structure prediction of non-coding RNA plays a crucial role in understanding the function of RNA.Eucalyptus grandis is a good fast-growing timber and multifunctional species present in the coastal zone of eastern Australia and belongs to the Myrtacea family.They can be usually used as greening species,which can also be widely used in the chemical industry and pharmaceutical field.At present,non-coding RNA in Eucalyptus grandis is less studied,the miRNA and lncRNA in leaf and stem of Eucalyptus grandis are the object of this paper.The systematic identification and analysis by bioinformatics method was made to analyze them,including sequence analysis,target genes prediction,the target genes functional annotation analysis etc.The main results are as followed:1 The leaf and stem of Eucalyptus grandis were used to do the small RNA high-throughput sequencing.After library construction,sequencing,filtering and selection,the potential miRNAs in different tissues could be obtained.There was 386 miRNAs could be obtained,including 179 miRNAs in leaf,257 miRNAs in stem and there was 50 common miRNAs between leaf and stem.2 The miRNA family,which was have the larger number and higher expression was MIR396.Under the phylogentic tree analysis and target gene functional annotation analysis,it could get that the function of MIR396 in Eucalyptus grandis was mainly participated in coding protein and regulation of cell grown.The three randomly selected members of MIR396 could all be validated by qRT-PCR.3 It was obtained 292 differentially expressed(DE)miRNAs under the differentexpression analysis between different plant organs in same species in this study.Under the KEGG annotation analysis of the miRNAs' target genes,the apparentest physiological process that miRNA was participated in stem was plant-pathogen interaction.The function of the miRNAs' target genes in this physiological process were related to the disease-resistant protein RPM1 and disease-resistant protein RPM2.4 The leaf and stem of Eucalyptus grandis were used to do the lncRNA high-throughput sequencing.After library construction,sequencing,splicing,filtering and selection,the potential lncRNAs in Eucalyptus grandis could be obtained.There was 551 lncRNAs could be obtained,including 124 special lncRNAs in leaf,130 special lncRNAs in stem and there was 297 common lncRNAs between leaf and stem.The 10 randomly selected lncRNAs could all be validated in leaf and stem of Eucalyptus grandis by qRT-PCR.5 It was obtained 158 DE lncRNAs under the different expression analysis between different plant organs in same species in this study.Under the GO annotation analysis of the down-regulated and up-regulated lncRNAs' target genes,the apparentest difference in biological process between them was oxidation-reduction process.Under the KEGG annotation analysis of the lncRNAs' cis-target genes and trans-target genes,the apparentest physiological process that lncRNA with different targeted way between leaf and stem were obtained,respectively.In the cis-target genes analysis,the highest related and reliable pathway of cis-target genes was the ubiquitin mediated proteolysis,and there was mainly collaborative regulation of the lncRNAs and target genes in the ubiquitin mediated proteolysis pathway.In the trans-target genes analysis,the main related pathways of trans-target genes were protein export,protein processing in endoplasmic reticulum and phagosome,the genes of them were same and related to the formation of Sec61 subunit alpha-like transport protein.The protein export and phagosome had the highest reliability.There was collaborative regulation between lncRNA and target genes in protein export,protein processing in endoplasmic reticulum and phagosome pathways.6 It could get the relationship of different non-coding RNA in stem through the similarity and complementarity analysis between miRNA and lncRNA in stem.The main relationship between miRNA and lncRNA in stem was as followed:(1)lncRNA was theprecusor to generate miRNA;(2)lncRNA was the miRNA's target;(3)lncRNA-miRNA competition for mRNA.In stem,the member of MIR396 family had the competitive relationship with the special lncRNA in stem.The function of common lncRNAs in different tissues was different and the special metabolism processes in different tissues in one individual may be regulated only by common lncRNAs.These results help us to further understand the functions of the non-coding RNA in Eucalyptus grandis. |
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