Chloroplast genomes of two Pueraria DC. species: sequencing, comparative analysis and molecular marker development

Abstract

Puerariae lobatae radix (Ge-Gen in Chinese) and Puerariae thomsonii radix (Fen-Ge) are widely used as medicine and health products, particularly in Chinese medicine. Puerarin and daidzein are the primary bioactive compounds in Puerariae radix. These isoflavones have been used to treat cardiovascular and cerebrovascular diseases, hypertension, diabetes, and osteoporosis. The content of puerarin in Ge-Gen is about six times higher than that in Fen-Ge, so its use has a higher pharmacological effect. It is therefore of great importance to effectively distinguish between these two species. However, because their basal plants, P. lobata (Willd.) Ohwi and P. thomsonii Benth., possess an extremely similar appearance, and detecting the level of chemical constituents is just a rough distinction, it is necessary to develop more efficient identification approaches. Here the complete chloroplast genomes of P. lobata and P. thomsonii were deciphered, including sequencing, assembly, comparative analysis, and molecular marker development. The results showed that they are 153,393 and 153,442 bp in length, respectively; both contain 124 annotated genes, including eight encoding rRNA, 29 encoding tRNA, and 87 encoding proteins. Phylogenetic analysis showed that they form a clade, indicating that they originate from the same ancestor. After obtaining 10 intergenic/intronic regions with a genetic distance greater than 0.5 cm, primers were designed to amplify regions of high variability in P. lobata and P. thomsonii. Finally, a 60-bp differential base fragment, located in the intron of rpl16, was developed as a molecular marker to efficiently distinguish between these two species.Puerariae lobatae radix, known as Ge-Gen in Chinese, is a popular traditional Chinese herbal medicine that was first described in the Shennong Herbal Classic. The genus Pueraria DC. belongs to the Fabaceae family and comprises about 20 species worldwide. It is mainly distributed in East Asian countries, among which China is the distribution center, accounting for 11 species. The dried roots of Ge-Gen have been widely used for the treatment of influenza, muscle stiffness, and other sicknesses [1]. Owing to a multi-origin traditional Chinese medicine, there are two Pueraria species: Pueraria lobata (Willd.) Ohwi and Pueraria thomsonii Benth., whose roots were considered the main source of Ge-Gen because of the wide distribution and

Complete Chloroplast Genome Sequences of Two Ehretia Trees (Ehretia cymosa and Ehretia obtusifolia): Genome Structures and Phylogenetic Analysis

“…The arrangement and recombination of the cp genome may be significantly influenced by the regions and the numbers of the repeat sequences [61]. The long repeat sequence analysis revealed that palindromic and forward repeats were the most common repeats in E. cymosa and E. obtusifolia (Figure 5), which is consistent with other angiosperm cp genome analyses [62][63][64][65][66]. The SSRs analysis showed that the cp genomes of E. cymosa and E. obtusifolia comprised 141 SSRs and 139 SSRs, respectively (Table 2).…”

Complete plastome genomes of three medicinal heliotropiaceae species: comparative analyses and phylogenetic relationships

“…The long repeat sequence analysis of E. strigosa , H. arbainense , and H. longiflorum recognized the forward and palindromic repeats were the most common repeats (Fig. 5 and Tables S9 , S10 , and S11 ), as found in the most angiosperm plastomes [ 60 – 64 ]. The number and regions of repeat sequences might influence the recombination and arrangement processes within the plastome [ 65 ].…”

Comparative Chloroplast Genomics Reveals a Unique Gene Inversion in Two Cordia Trees (Cordiaceae)

“…The number and regions of repeat sequences might be the reason for the recombination and arrangement events in the chloroplast genome [71]. The palindromic and forward repeats are the dominant types of repeats in the angiosperm plastomes [72][73][74]. The SSRs analysis revealed that both genomes contained 155 microsatellites (Table 2).…”