Genomes of Complete Chloroplast of Valuable Toona Species:Basic Features,Comparative Analysis and Phylogenetic Evolution in Meliaceae

[Objective]Toona is a highly economically valuable genus which has an extensive range of genetic resources.Effective identification of germplasm resources is crucial for carrying out breeding work because of the underexploitation of its resources and the high degree of similarity of its physical traits.Chloroplast genome(cp)genome is typified by evolutionary slowness and structural conservation.Toona ciliata(TC)and Toona sinensis(TS)were chosen from qualitied germplasm resources for high-throughput sequencing,plus publically available data of Toona ciliata var.Pubescens(TCv)to enable researchers to examine the properties of the various cp genomes of Toona essential species.[Method]With the tools of Cp-omics,we conducted genome mapping,repetitive sequence,codon preference,and snp/indel in 3 highly valuable species,combined with NCBI downloads of the complete genomes of Toona species to conduct IR/SC boundary and high marginal region analysis,maff sequence alignment,and phylogenetic research.[Result]Consequently,the cp genome was 159139-159618 bp in length,with a typical cp tetrad structure,all with a genomic GC content of nearly 37%,and encoding a total of 125-138 functional genes.The number of long repeat sequences are not equivalent,mostly distributed in Intergenic Space,and in simple sequence repeats at 54-60bp,dominated by single and dinucleotide repeats.Codon Usage bias has A/T preference,whilst 31 codons had RSCU values greater than 1,MILC and SCUO were nearby 0.565151-0.573785 and 0.300127-0.303655 and were corroborative.In reference to T.sinensis,T.ciliata var.pubescen and T.ciliata were excavated to 113 and 115 snp,151 and 127 indel,respectively.Within the IR/SC border,despite a certain consistency between T.ciliata and several variants,there are still more variants due to the expansion and contraction of single copy regions.The variant intervals were focused on non-coding regions,mutation hotspots such as petB-petD,trnC-petN-psbM,trnT-trnF-ndhJ,ndhC-trnM,trnS-trnR,trnC-petN-trnD and ndhF-rpl32-trnL were found,nucleotide diversity analysis screened for highly variable interspecies intervals such as ccsA-ndhD,7 SNP loci were selected in variant fragments as markers that could be applied for species identification,the phylogenetic tree of the Toona showed close affinities.[Conclusion]This work is of great significance for the development and identification of germplasm resources,breeding of superior species,systematic classification and evolutionary relationships of Toona.