The Functional Comparative Analysis Investgaytion Of Conserved And Non-Conserved Lncrnas In Upland Cotton

Hybridization and polyploidization,which cause genome shock through noncoding transcriptome re-programming,have major impacts on genome evolution.Almost all angiosperms have undergone one or more polyploidy events in evolution.And allotetraploid cotton is an important economic and fiber crop out of polyploidy events.Polyploid cotton tend to be big,including large fruit,improved seed index,high yield in the morphology.Gossypium hirsutum and G.barbedense have been continuously domesticated and widely planted worldwide due to high yield and adaptability.The molecular mechanisms of the positive effects of interspecific hybridization and polyploidization are not well understood.Long non-coding RNA（lncRNA）showed strong expresion specificity among cotton species,mainly due to the reprogramming of expression in the process of distant hybridization and polyploidization.The difference of transcriptional behavior patterns and regulatory functions between conserved lncRNAs and non-conserved lncRNAs which have extremely expression variations during hybridization and polyploidization is still unknown.This study conducted a preliminary study on the formation of hybrid and polyploidy advantages and the molecular regulation mechanism of lncRNA based on the conserved differences of lncRNA.To unveil the biological effects of lncRNAs reprogrammed by genome shock,we analysis the genome and transcriptome of G.arboretum（A2）,G.raimondii（D5）and Upland cotton genetic standard line G.hirsutum（AD1）.LncRNAs of upland cotton were classified into 607 conserved lncRNAs and 5910 non-conserved lncRNAs according to the sequence similarity and collinlinearity between the diploid and tetraploid cotton genomes.Comparative genomic analysis,weighted gene coexpression network analysis（WGCNA）and virus induced gene silencing（VIGS）of lncRNAs showed that lncRNAs response to different abiotic stresses more actively and specificity comparing with protein coding genes（PCGs）.Non-conserved lncRNAs tended to be overlapped with the flanking protein coding genes（PCGs）than conserved lncRNAs.Non-conserved lncRNAs were preferentially positively associated with the expression of flanking PCGs.We found that conserved lncRNA and non-conserved lncRNA may both have regulatory functions of growth and development and abiotic stress tolerance via a high throughput functional screening with 100 lncRNA candidates.The pilot functional investigation of a conserved lncRNA XLOC₂27558 and a nonconserved lncRNA XLOC 148490 were performed.In general,the stronger the nitrogen metabolism and transport capacity of plants,the better the drought resistance of plants.Current results suggest that XLOC₂27558 may have a trans-regulation on a protein-coding gene which acting on the nitrogen anabolic pathway.XLOC₁48490 is a non-conserved lncRNA,generated by transcription activation due to DNA methylation level changes which caused by the deletion and mutation of large DNA fragments during the process of cotton WGD.This structural difference in chromatin may have a cis-regulation of a neighboring gene encoding choline monooxygenase which is a key enzyme in the synthesis of betaine.The difference in the expression activity of choline monooxygenase may directly affect the function of its protein encoding,and participate in the drought regulation of cotton by affecting the osmotic pressure of plants under drought stress.The two functional lncRNAs metioned above demonstrated that lncRNAs can take a part in drought tolerance control through either cis-or trans-regulation.In particular,novel lncRNAs can be activated by genome shock and can develop new functions that are beneficial for environmental adaptation.Our data suggest the lncRNAs have an application potential on crop improvements towards the improvement of abiotic stress tolerance.