Identification And Characterization Of Long Non-coding RNAs In Nilaparvata Lugens And Plutella Xylostella

Long non-coding RNAs(long ncRNAs,lncRNA)are defined as non-protein coding transcripts longer than 200 nucleotides.In recent years,IncRNA researches have become the hotspot of current research.LncRNA involve in genomic imprinting,X chromosome silencing,chromatin modification,transcriptional activation,transcriptional interference,nuclear transport,growth and development and other important regulatory processes.With the accumulation of high-throughput sequencing data,the improvement of the IncRNA prediction pipeline,the IncRNAs of fruit flies,bees and other 10 insects have been identified.In this paper,the prediction pipeline for predicting insect lncRNA was constructed and optimized,and then was used to predict the lncRNA of Nilaparvata lugens and Plutella xylostella.The results are as follows:1.Discovery and characterization of Long Non-coding RNA of Nilaparvata lugensFour transcriptome of the N.lugens including Hangzhou strain,Taichung strain,the female salivary gland and the third instar nymphs were collected from NCBI SRA database.The transcriptome were assembled using HISAT2 and StringTie.The 2,386 IncRNA genes of brown planthopper was predicted.The results showed that the IncRNA of brown planthopper was the same as that of the previous reported,and was similar to that of human,nematode and zebrafish lncRNA,and contained two exons with a relatively high percentage of transcripts.The average length of protein coding genes was 1,106 bp whereas that of lncRNA transcript was significantly shorter,only 596 bp.In addition,about 12.2%of the lncRNA of brown planthopper were alternative spliced.Some of the lncRNA genes were transcribed with many transcripts,which may be related to IncRNA transcription dynamic expression is relevant.2.The discovery and characterization of long non-coding RNA of Plutella xylostellaThirteen RNA-Seq data of different developmental stages population(larvae,larvae,pupae,adults),the parasitic population(Plutella xylostella was parasitic by Diadegma semiclausum and control),the Bt protein resistance group(Cry1Ac susceptible and resistant midgut tissue)and different pesticide resistant populations(chlorpyrifos and fipronil resistance)of the diamondback moth(P.xylostella)were downloaded In the NCBI SRA database.A total of 2,639 lncRNA genes were found.The results showed that the IncRNA of P.xylostella was similar to that of brown planthopper,human,nematode and zebrafish,and the two exons contained a relatively high percentage of transcripts.Compared with the protein coding gene,the length of transcript was significantly shorter.Expression analysis showed that there were 31 differentially expressed IncRNAs in the midgut of susceptible and Cryl Ac resistant strain.Compared with control,11 differentially expressed IncRNAs were found in the parasitic group.In the transcriptome of eggs,larvae,pupae,adults,a total of 160 lncRNA showed differences in expression.In addition,two IncRNAs of TCONS 00147638 and TCONS 00147639 were custered in the minus chain of intron of Px013127 and was co-expressed in different developmental stages.Two IncRNAs TCONS 0013670 and TCONS 0013672 existed in the intergenic region were also co-expressed in the control and parasitic group.3.Strand-specific sequence of IncRNA of Plutella xylostellaTo determine the reliability of identified IncRNA,10 IncRNAs were randomly selected and the sequence was verified by strand-specific PCR.The results of electrophoresis showed that 8 of the 10 lncRNAs were consistent with the prediction,and the sequencing confirmed the results.8 lncRNAs were validated at the direction of 3 'end.The other two were not amplified.