Structural Variation And Evolutionary Analysis Of Chloroplast Genome TRNA In Plants

Plant chloroplasts have a circular double-stranded genome that carries many genes coding for self-regulation.tRNA is an important evolutionarily conserved gene family with a typical clover secondary structure,which is mainly responsible for protein translation and amino acid transport.However,the structural characteristics and evolutionary mechanism of tRNA in plant chloroplast genomes are not clear.In this study,the chloroplast genomes of 122representative plants from 6 phylum of the plant kingdom were selected to identify and analyze the structural variation,spatial configuration and evolutionary characteristics of the chloroplast tRNA genes.The main research results are as follows:1.A total of 4057 tRNA sequences were identified and extracted from 122 plant chloroplast genomes.The length of its tRNA ranged from 56-93nt,with an average length of 77nt,and the longest tRNA was all tRNA^Ser.The number of tRNA encoded in chloroplast genomes of plants ranged from 26 to 37,among which the number of tRNA encoded in chlorophyta was the least(26)and the number of tRNA encoded in angiosperm was the most(37).The number of D-loop and variable region nucleotides in the secondary structure of chloroplast tRNA varied the most,and the number of D-loop nucleotides ranged from 7 to 12bp.The number of nucleotides in the variable region ranged from 2 to 24bp.The number of nucleotides in acceptor arm,D-arm,anticodon arm,anticodon loop,?arm and loop were 7,4,5,7,5 and7bp.The number of?loop nucleotide was completely conserved at 7bp.The tRNA sequence comparison revealed that only the?loop contains a more conservative consensus sequence,and the variation characteristic of the loop was U-U-C-x-A-x₂.The first nucleotide of the acceptor arm was dominated by G,the first and last nucleotide of the D loop were dominated by A,the last two of the anticodon loop were dominated by A-A,and the last two of the?arm were dominated by G-G.Precoded C-C-A tails were found in a small number of 3?terminal nucleotide sequences of tRNA^Arg(ACG),tRNA^Ala(UGC),tRNA^Leu(UAA),tRNAA^Lys(UUU),tRNA^Ile(GAU)and tRNA^Tyr(GUA).Four special tRNA types were found in this study,namely,lack of acceptor arm,anticodon loop contains 9 nucleotides,variable region and anticodon loop have the same number of nucleotides,both are 7 nucleotides,anticodon was tRNA^Ileof CAU.The tRNA in plant chloroplast genome contains 22-33 anticodon.Phylogenetic analysis showed that tRNA in chloroplast genome evolved from multiple common ancestors,and tRNA^Ile(CAU)evolved from tRNA^Met(CAU).The chloroplast tRNA transition rate was higher than the transversion rate.In the course of evolution,tRNA experienced more loss events.2.Predict the tertiary structure of 4 types of tRNAs(Ala,fMet,Gln and Phe)from 11representative species,and found that the tertiary structure of all tRNAs is relatively conservative and presents an L-shaped spatial shape.At the same time,the four parts of tRNA(?loop,acceptor arm,variable region and anticodon loop)were compared and analyzed for the tertiary structure.It was found that the?loop had the most conservative nucleotide sequence and length,but the spatial structure was not conservative,the most conservative is the three dimensional structure of the acceptor arm,which may be related to the accuracy and stability of the amino acid carried,and the spatial structure of the variable region changes the most.The comparative analysis of different plant groups found that from lower to higher plants,the chloroplast tRNA content increased,the length was stable overall,and only conservative sequences existed in the?loop region;the tertiary spatial structure of the same type of tRNA was similar,and the acceptor arm region of the spatial structure,the most conservative,these results provide an important basis for a deep understanding of the evolutionary characteristics and laws of chloroplast tRNA in the evolution of plants.