Abstract:
To explore the characteristics and codon usage bias of the whole chloroplast genome(chloroplast DNA, cpDNA) of Amomum maximum, this study used the Illumina HiSeq sequencing platform to sequence the whole chloroplast genome of A. maximum, and obtained the complete chloroplast genome sequence through assembly and annotation. The microsatellite sites, codon bias and phylogeny of the chloroplast genome of A. maximum were analyzed by software such as MISA, IQTREE and CodonW. The results showed that the complete chloroplast genome of A. maximum was 163 602 bp in length, with an average G+C content of 36.1%. The lengths of the large single copy(LSC) region and the small single copy(SSC) region were 88 626 bp and 15 426 bp, respectively, and the two inverted repeat(IR) regions were 29 775 bp. The chloroplast genome of A. maximum encoded 132 genes, including 86 protein-coding genes, 38 tRNA genes and 8 rRNA genes. A total of 132 simple sequence repeat(SSR) sites were detected on the chloroplast genome sequence. Among them, the numbers of mononucleotide, dinucleotide, trinucleotide, tetranucleotide and pentanucleotide were 65, 35, 5, 24 and 3, respectively, most of which belonged to the A/U type of single base repeat. Phylogenetic analysis showed that A. maximum was clustered as a separate branch in the genus Amomum. This laid a foundation for the research of identification, evaluation and species formation mechanism of A. maximum germplasm resources.