Comparison of chloroplast genome characteristics and phylogenetic analysis between Themeda japonica and two species of Themeda

Abstract

Objective Themeda japonica was used as the experimental material to compare its chloroplast genome characteristics with those of two congeners, T. triandra and T. quadrivalvis, and their phylogenetic relationships with the closely related species. Methods Using the Illumina HiSeq high throughput sequencing platform, the chloroplast genome of T. japonica was sequenced for the first time. SPAdes and CpGAVAS2 were used to assemble and annotate it, respectively. CodonW, DnaSP, and MISA were used to perform a series of comparative genomic analysis with two species of plants of the same genus, and the maximum likelihood (ML) method was used to construct a phylogenetic tree. Results The three chloroplast genomes were 138 735—138 961 bp in length, with a typical tetrad structure, and a total of 129 genes were annotated; compared with the two species of the same genus, the inverted repeats (IR) contracted by 2 132 bp, the large single copy region (LSC) expanded by about 4 000 bp, and the small single copy region (SSC) did not change much. Codon preference analysis showed that the codons with the highest and lowest relative abundance in the three chloroplast genomes were the same, while the relative abundance of synonymous codons was slightly different, but the difference was not significant. Nucleic acid polymorphism analysis showed that the nucleic acid polymorphism values (Pi) of the sequences in the inter-region of the three chloroplast genomes were generally higher than those of the shared gene sequences, and the IR region was more conserved than the LSC and SSC regions. A total of 38, 36 and 37 simple sequence repeats (SSR) and two long sequence repeats were detected in the three chloroplast genomes, respectively. Phylogenetic analysis indicated that T. japonica was most closely related to T. triandra. Conclusion The comparative analysis of chloroplast genome characteristics and phylogeny between T. japonica and two species of Themeda was carried out, laying the foundation for the species identification of the three species and the study of genetic diversity and phylogeny of Themeda.