Characteristics of chloroplast genome and phylogenetic analysis of alpine plant Rhodiola tangutica (Crassulaceae) postprint

Abstract: In order to explore the structure characteristics, gene information and phylogenetic relationship of the chloroplast genome for Rhodiola tangutica, which is an important medicinal plant growing in Northwest China, this study sequenced its complete chloroplast genome using the high-throughput sequencing technology with Illumina NovaSeq6000. We analyzed the genome structure, gene function and genetic relationship of the chloroplast genome based on NOVOPlasty, GeSeq, PGA, IRscope and MISA. The results were as follows: (1) The chloroplast genome of R. tangutica had a typical and quadripartite circular structure of 150 863 bp in length, including LSC (82 121 bp), SSC (16 996 bp) and IR (25 873 bp). Total GC content was 37.8%, among which the IR regions had the highest (42.9%). The genome encoded 131 genes in total, including 85 PCGs, 38 tRNAs and eight rRNAs. (2) Among the 32 471 codons, cysteine (Cys) had the smallest percentage (1.18%), while isoleucine (Ile) had the highest (8.24%). There were 29 codons with the value of RSCU above one. (3) The analysis of IR regions showed that both rps19 and ndhF were expanded into the IRB region. (4) Phylogenetic analysis indicated that R. tangutica and R. quadrifida had the closest relationship. Estimates of divergence times indicated that the origin of Rhodiola species was estimated to be around 15.50 Mya (95% HPD: 6.0-21.0 Mya). In this study, we clarified the chloroplast genome characteristics of Rhodiola tangutica and obtained a reasonable phylogenetic relationship of Rhodiola, which provided a theoretical basis for the study of genetic diversity, the discussion of adaptive evolutionary mechanism and the protection of germplasm resources of Rhodiola.