Complete Chloroplast Genome of Calligonum Mongolicum: Genome Organization, Codon Usage Pattern, Phylogenetic Relationships, Comparative Structure and Adaptive Evolution Analysis

Abstract

Background The perennial shrub of Calligonum mongolicum 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 and genome evolution in related plant families. In the present study, the complete cp genome of C. mongolicum was sequenced, and the characteristics were described, then the genomic structure was compared to other three Polygonaceae species.Results 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 exhibited A/T preference, and 7 codons were identified as the optimal codons. Multivariate statistical analysis of parity rule 2, ENC-plot, and neutrality plot were combined conducted to imply natural selection as the crucial constraint in SCU bias in C. mongolicum cp genome.The phylogenetic tree showed that Rumex acetosa was the most related plant to C. mongolicum. 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 species in the Polygonaceae, the borders of IRb/SSC and SSC/IRa in C. mongolicum changed greatly. Furthermore, adaptive evolution analysis of 75 orthologous protein-coding genes indicated that only the psbK gene was under positive selection, which might be crucial in the adaptive evolution of C. mongolicum.Conclusions Our results comprehensively depicts 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.

Comparative chloroplast genome analyses of Paraboea (Gesneriaceae): Insights into adaptive evolution and phylogenetic analysis

“…PSBK is not necessary for the assembly or activity of photosystem II complex, but is essential for optimal photosystem II function. The psb K gene was detected under positive selection in Echinacanthus (Acanthaceae) and Calligonum Mongolicum (Polygonaceae), and speculated to play an important role in plant adaptation evolutionary process to the diverse environment ( Gao et al., 2019a ; Duan et al., 2020 ). The ndh F gene encodes NADH dehydrogenase subunit protein ( Kubicki et al., 1996 ).…”