Analysis Of Long Inverted Repeats In Plants,as Well As The Update Of Rice Functional Genes Database

Small RNAs play a crucial role in plant genomes,whose sizes range from 18 to 30 nucleotides.Long inverted repeats(LIRs)can be transcribed into hairpin RNAs(hp RNAs),which can be further processed into small interfering RNAs(si RNAs).We identified LIRs in 55 plant genomes including Arabidopsis,rice,and maize.We found significant variations in LIRs in different genomes of rice and maize;the greater genetic distance,the greater difference in LIRs.Meanwhile,the small RNA sequencing data in the published literature were collected and aligned to the identified LIRs in different genomes.In this way,we aim to quantify the expression of LIRs in different tissue stages,identify key genes regulating the processing of LIRs into si RNAs,and dissect LIRs related to rice stress.We found that DCL1、DCL2、DCL3 and AGO1、AGO2、AGO4 as well as RDR6、MEL1、HEN1,etc.may play important roles in the formation of si RNA from LIR.Furthermore,a candidate LIR involved in H2O2 stress resistance was identified in rice based on the sequencing data of a rice accession under abiotic stress.We further identified a candidate LIR with regulatory roles in blight disease resistance.These results indicate that several LIRs and the derived small RNAs may play a key regulatory role in the process of biological and abiotic stresses in rice,which provides a foundation and direction for further studies on the synthesis process and function of si RNA formed by LIRs.Rice is one of the important food crops in the world.It is also a model plant to study the functional genomes of monocotyledonous plants.Understanding the function of each gene in rice genome is very important for the genetic improvement of rice germplasm resources.We established a comprehensive and accurate database containing more than 4,100 functionally characterized rice genes and more than 6,100 members of different gene families by integrating data from existing database and consulting published articles of rice functional genome research studies,which can facilitate investigating rice functional genes.We constructed an interaction network of 1,281 genes based on the relationships among 2,819 genes and found that the genes related to flowering are the largest component of the interaction network.At present,all the collected data with are stored in fun Rice Genes database(https://funricegenes.github.io/).We further used R/Shiny to build an interactive application for the database(https://venyao.xyz/fun Rice Genes/).In addition,we provided several functions that are unavailable on the static website,such as BLAST and gene ID conversion.Users can also update new genes and related information through the interactive application.