Comparative Analysis of the Complete Chloroplast Genomes in Toona Sinensis and Toona Ciliata: Phylogenetic Relationship of Toona

Abstract Taking the chloroplast genomes of Toona sinensis (GenBank:OK572965) and Toona ciliata (GenBank:OK572964.1) as the research objects, the structural characteristics and phylogenetic relationship of their chloroplast (cp) genomes were researched. Here, we sequenced the complete chloroplast genome sequence using Illumina HiSeq high-throughput sequencing technology via a combination of annotations and simultaneously compared their cp genome structure features. Codon usage bias was aligned with the previously reported Azadirachta indica (KF986530), together with IR boundary analysis with other investigated relatives, and complete genome sequences were compared to each other to construct maximum likelihood (ML) phylogenetic trees. The results showed that (1) the chloroplast genomes of Toona sinensis and Toona ciliata exhibited typical quadripartite and circular structures that were relatively conserved in genomic structure and the synteny of gene order; both Toona sinensis and Toona ciliata annotated 125 genes, including 88 protein-coding genes (PCGs), 29 transfer RNAs (tRNAs) and 8 ribosomal RNAs (rRNAs). (2) Fifteen and 13 palindromic repeats, 10 and 15 forward repeats and a single complementary repeat were detected in the chloroplast genomes of the two species. At the same time, 61 and 55 SSRs were identified, respectively, which were primarily located in the coding interval. There was a significant codon preference in the genome, with codons that end in A and T used much more frequently than synonymous codons. (3) IR boundary and sequence divergence analyse found some candidate fragments to identify the selected related species, such as trnH, ycf1,etc. (4) A phylogenetic tree was constructed using the maximum likelihood (ML) method, and the results revealed that Toona sinensis and Toona ciliata clustered into a single independent branch with high support. This investigation has established a theoretical foundation for plant identification, molecular marker development, conservation efforts, population dynamics and further study of phylogenetic processes. The availability of chloroplast genomes provides valuable genetic information for accurate identification, taxonomy, and phylogeny and contributes to the exploration and utilization of plants.