Complete Chloroplast Genomes from Sanguisorba: Identity and Variation Among Four Species

Abstract

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

“…mVISTA revealed a low divergence between the genomes of the five Dicliptera species, suggesting that the cp genomes were conserved. The IR regions were more highly conserved than the SC regions and the coding regions were less variable than the non-coding regions, which is also found in other angiosperms (Gao Deng, 2018; Meng et al, 2018;Li, Zhao & Liu, 2018;Yan et al, 2019). Khakhlova & Bock (2006) suggested that gene divergence with less variability in the IR and coding regions may be a result of copy corrections during gene conversion, which can correct or delete the mutation.…”

“…These structures are longer than the cp genome of A. paniculata (15,249 bp) (Ding et al, 2016). The genome size of all Dicilptera is relevant to LSC variation (Table 2) and this phenomenon has also been identified in other species (Zhao et al, 2018;Li, Zhao & Liu, 2018;Meng et al, 2018). mVISTA revealed a low divergence between the genomes of the five Dicliptera species, suggesting that the cp genomes were conserved.…”

“…The non-synonymous (K A )/synonymous rate (K S ) ratio (ω = K A /K S ) provides a measure of selective pressure at the amino acid level. As suggested by Makalowski & Boguski (1998), the ω values less than one (K A /K S <1) indicate that the gene is under negative selection and vice versa (Wojciech & Mark, 1998;Meng et al, 2018). Recent studies have detected many positively selected chloroplast genes (K A /K S >1), such as the ndhC, ndhJ,psbK,psbN,rpl14,rpl16,rps4,rps15,rps18,rps19,infA,and rpoB genes in Echinacanthus and the petA,psbD,psbE,ycf3,psaI,rps4,psbM,ndhE,ndhG and rpoC1 genes in Allium (Gao, Wang & Deng, 2018;Xie et al, 2019).…”

“…The chloroplast genome (cp genome) is an independent genome that has been used in many evolutionary studies (Fan et al, 2018;Gao, Wang & Deng, 2018;George et al, 2015;Chen et al, 2018;Inkyu et al, 2018;Kim & Lee, 2004;Wang et al, 2016;Mader et al, 2018;Meng et al, 2018;Ma et al, 2017;Raubeson et al, 2007;Wang et al, 2008;Wu et al, 2018). It has a simple structure with a low molecular weight and multiple copies.…”

“…Most of the cp genomes have circular structures with quadripartite organizations composed of one large single copy region (LSC), one small single copy region (SSC), and a pair of inverted regions (IRs). However, there are numerous exceptions to the common structure, like the IR-lacking clade (IRLC) in Fabaceae (Fan et al, 2018;Gao, Wang & Deng, 2018;George et al, 2015;Chen et al, 2018;Inkyu et al, 2018;Kim & Lee, 2004;Wang et al, 2016;Mader et al, 2018;Meng et al, 2018;Schwarz et al, 2015). The complete cp genomes of more than 2,400 plants have been published, to date, in the NCBI database (http://www.ncbi.nlm.nih.gov/genome).…”