Study Of Non-coding RNAs In Gossypium Arboreum Based On Multi-omics Data

There are a large number of non-coding regions in the genome of eukaryotes.In recent years,more and more studies have confirmed that a large number of transcription events occur in these non-coding regions,and even some transcripts can be translated.These non-coding RNAs and the small peptides encoded by them have also been reported to regulate the organism development in various forms.As an important material for textile products,cotton fiber,the role of non-coding RNA in its growth and development is still unclear.Therefore,in this article,we made a comprehensive and systematic assembly annotation of the long noncoding RNA(lncRNA)of Gossypium arboreum;Meanwhlie,we tried to study the translational event in lncRNA and UTR(untranslated region)of protein coding genes based on ribo-seq and mass spectrum.Finally,we got six main results below:(1)By integrating the four transcriptome sequencing data of Pac Bio-seq,ss RNA-seq,CAGE-seq and PAS-seq,we compiled a process method named PULL(Plant Full-length lncRNA Identity),and finally 9,240 lncRNAs with accurate transcription start and stop information were identified from 21 tissue samples in Gossypium arboreum.(2)The characteristics of the promoter and terminator of lncRNA with accurate transcription start and stop site information indicate that the transcription of most lncRNA depends on RNA polymerase(Pol)II.And some lncRNAs have alternative usage of TSS(Transcription Start Site)and TES(Transcription End Site)during development stage.(3)The expression analysis proves that lncRNA exhibits a strong tissue-specific expression pattern;and it can regulate the expression of surrounding protein coding genes in cis.(4)We found a specific lncRNA lnc-Ga13g0352 that was up-regulated at the initial stage of cotton fiber development,and verified the combination and regulation of the target genes by Ch IRP-seq(Chromatin Isolation by RNA Purification sequencing).(5)Baed on ribo-seq and mass spectrum,we found that part of lncRNAs can be translated;meanwhile,the evidence of translation was also found in the 5 ’and 3’UTR of some protein coding genes.Besides,the translation of UTR could regulate the translation of downstream m ORF.(6)Based on the integration of genomic and transcriptome RNA-seq in public databases,especially the Ribo-seq and mass spectrometry data from public database,we built a pipeline to identify sORFs in 35 different plant species including Chlamydomonas reinhardtii,Arabidopsis thaliana,cotton(Gossypium arboreum),Oryza sativaand Zea mays.And based on the results,we designed a web-accessible database,PsORF(http://psorf.whu.edu.cn/).