Comparative Genomic Analysis Of Arabidopsis Thaliana And Maize

Long noncoding RNA (lncRNA) is new type of RNAs which have a long sequence more than 200nt and lack coding potential. They can regulate gene expression at transcriptional and post-transcriptional levels as signals, decoys, guides and scaffolds. Plant lncRNAs play various roles and participate in many biological processes, especially in reproductive development and response to stress. With the rapid development of high-throughput sequencing technologies, more and more lncRNAs have been found or being found in plants. However, the current studies focused on the preliminary identification and function of lncRNAs, analysis on transcriptional regulation about lncRNAs was seldom.Arabidopsis thaliana and Zea mays are the model plants of biological research. A large amount of data has been accumulated for their physiological, biochemical, genetic, genome and transcriptome and lncRNAs, and this make the analysis of their lncRNAs possible. This article based on genomics and comparative genomics and using sequence and conservation, polymorphism and evolution, and promoter analysis to reveal transcriptional regulation and molecular evolution mechanisms of lncRNAs. Our results show that:1. The sequence characteristics results show that the length distribution of the A. thaliana and maize lncRNAs is not centralized, base composition and GC content are also different significantly.2. We aligned the A. thaliana lncRNAs with maize lncRNAs and found conservation of lncRNAs between the two species is very poor. Then we analysis the conservation of lncRNAs among five species that close related with A. thaliana. The result shows that only 30 of 2708 lncRNAs (11.1%) are found in five species and conservation is also low.3. In this study, we use two methods respectively to predict transcription start site of lncRNAs in A.thaliana and maize. Full-length cDNA available was employed to precisely predict the accurate position of lncRNA TSS in A.thaliana and maize based on known lncRNAs. In all, only 14 and 38 TSSs of lncRNAs were obtained in A.thaliana and maize, respectively. Then we analysis the GC-skew of lncRNAs upstream area in two species, TSSs of 2356 and 660 IncRNAs in A.thaliana and maize predicted by analysis of GC-skew of upstream region of lncRNAs.4. After conservation analysis of lncRNAs among five species that have close genetic relationship with A.thaliana, we obtain 30 lncRNAs with high conservation which can be classified into 29 categorys as only two lncRNAs are a kind of classification. We use adjacency method (N-J) in MEGA6.0 to build the evolutionary tree, then choose two specific lncRNAs to build the evolutionary tree respectively. Evolutionary analysis of lncRNAs suggests that conservation of lncRNAs is poor and lncRNAs homology among close related species is not high either. lncRNAs have a rapid evolution.Conclusion:the sequence analysis of lncRNAs in A.thaliana and maize showed that the conservation of the lncRNAs between species is very poor. Even among the arabidopsis and five species that close related with A.thaliana, the result shows that only 30 of 2708 lncRNAs (11.1%) are found in five species and conservation is also low. Promoter analysis results show that there are 146 cis-acting elements in both arabidopsis thaliana and maize, after classifying cis-elements, a total is divided into eight kinds of cis-elements, including environmental stress-related elements, hormonal responses-related elements, light cycle-related elements, devolepment related elements, promoter related elements, sites binding-related elements, other elements and unknown function elements. We found the cis-acting elements function on many aspects of plant biology, including the circadian clock, interacting with the environment, stress responses, regulation of growth and development by phytohormones. Our results provide a rich source of resources for the further study of lncRNAs transcriptional regulation and function.