Complete chloroplast genome of Calligonum mongolicum Turcz. and comparative analysis with other Calligonum species

The perennial shrub of Calligonum mongolicum Turcz. is a dominant native plant in all Calligonum species, which has the largest and most widespread geographic distribution in arid deserts of northern China. Understanding the phylogenetic relationship between C. mongolicum and closely related plant species will offer guidance on the classification and identification of inter-species and their varieties. The chloroplast (cp) genome is an optimal model to decipher phylogenetic relationships in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced and compared with other Calligonum species. The cp genome of C. mongolicum was 162,124 bp in length with a quadripartite structure. A total of 131 functional genes were annotated, 14 different genes of which harbored introns and exons, 50 long repeat sequences and 244 simple sequences repeats were identified. Synonymous codon usage (SCU) analysis of C. mongolicum and other 8 Calligonum species exhibited similar change patterns, and natural selection would be crucial for SCU bias in all the 9 Calligonum species. The phylogenetic tree showed that C. mongolicum was clustered closely to Calligonum species. From the comparative analysis of genomic structures, the inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions was relatively conserved than non-coding regions. Compared to other Calligonum species, the IR region of C. mongolicum had a slight contraction. Our results comprehensively depict the architecture of C. mongolicum cp genome, and will lay a vigorous foundation for further study on molecular marker selection, phylogenetic analysis, and population researches in Calligonum species.