High level of intraspecific divergence and low frequency of RNA editing in the chloroplast genome sequence of Tagetes erecta

Long-Lasting Silver Nanoparticles Synthesized with Tagetes erecta and Their Antibacterial Activity against Erwinia amylovora, a Serious Rosaceous Pathogen

A rapid, eco-friendly, and simple method for the synthesis of long-lasting (2 years) silver nanoparticles (AgNPs) is reported using aqueous leaf and petal extracts of Tagetes erecta L. The particles were characterized using UV-Visible spectrophotometry and the analytical and crystallographic techniques of transmission electron microscopy (TEM). The longevity of the AgNPs was studied using UV-Vis and high-resolution TEM. The antibacterial activity of the particles against Erwinia amylovora was evaluated using the Kirby-Bauer disk diffusion method. The results were analyzed using ANOVA and Tukey's test (p ≤ 0.05). Both the leaf and petal extracts produced AgNPs, but the leaf extract (1 mL) was long-lasting and quasi-spherical (17.64 ± 8.87 nm), with an absorbance of UV-Vis λmax 433 and a crystalline structure (fcc, 111). Phenols, flavonoids, tannins, and terpenoids which are associated with -OH, C=O, and C=C were identified in the extracts and could act as reducing and stabilizing agents. The best antibacterial activity was obtained with a nanoparticle concentration of 50 mg AgNPs L-1. The main contribution of the present research is to present a sustainable method for producing nanoparticles which are stable for 2 years and with antibacterial activity against E. amylovora, one of most threatening pathogens to pear and apple productions.

Intraspecific Chloroplast Genome Variation and Domestication Origins of Major Cultivars of Styphnolobium japonicum

Styphnolobium japonicum is a significant resource of ornamental and medicinal plants. In this study, we employed high-throughput sequencing to assemble nine chloroplast genomes of S. japonicum. We compared and reconstructed the phylogenetic relationships of these genomes, along with three publicly available chloroplast genomes. Our results showed that the length of the 12 S. japonicum chloroplast genomes ranged from 158,613 bp to 158,837 bp, all containing 129 unique functional genes. The genetic diversity within S. japonicum chloroplast genomes was relatively low, with π = 0.00029, Theta-W = 0.00028, and an indel frequency of 0.62 indels/1 kb. Among the four regions, the SSC region exhibited the highest genetic diversity and indel frequency, while the IR region had the lowest. Non-coding regions displayed greater genetic variation compared to coding regions, with a few highly variable regions identified. The phylogenetic tree constructed revealed that the major cultivars of S. japonicum originated from two genetic 'sources. S. japonicum 'JinhuaiJ2' had an independent origin and showed close relatedness to S. japonicum var. violacea, S. japonicum var. japonicum, and S. japonicum f. oligophylla. On the other hand, other major cultivars shared a common genetic origin and were closely related to S. japonicum f. pendula. This study highlights the variability of chloroplast genomes within S. japonicum and provides insights into the genetic origins of major cultivars and their relationships with different varieties and forma.

The chloroplast GATA-motif of Mahonia bealei participates in alkaloid-mediated photosystem inhibition during dark to light transition

Mahonia bealei and Mahonia fortunei are important plant resources in Traditional Chinese Medicine that are valued for their high levels of benzylisoquinoline alkaloids (BIAs). Although the phytotoxic activity of BIAs has been recognized, information is limited on the mechanism of action by which these compounds regulate photosynthetic activity. Here, we performed comparative chloroplast genome analysis to examine insertions and deletions in the two species. We found a GATA-motif located in the promoter region of the ndhF gene of only M. bealei. K-mer frequency-based diversity analysis illustrated the close correlation between the GATA-motif and leaf phenotype. We found that the GATA-motif significantly inhibits GUS gene expression in tobacco during the dark-light transition (DLT). The expression of ndhF was downregulated in M. bealei and upregulated in M. fortunei during the DLT. NDH-F activity was remarkably decreased and exhibited a significant negative correlation with BIA levels in M. bealei during the DLT. Furthermore, the NADPH produced through photosynthetic metabolism was found to decrease in M. bealei during the DLT. Taken together, our results indicate that this GATA-motif might act as the functional site by which BIAs inhibit photosynthetic metabolism through downregulating ndhF expression during the DLT.

A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms

Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of E. maackii. By combining this genome with seven available cp genomes from Euonymus species, we performed plastome variation analysis of E. maackii and Euonymus. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of E. maackii. The newly assembled cp genome of E. maackii was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of E. maackii, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including trnV-UAC, petN, ycf1-ndhF, trnM-CAU-atpE, rpl2-rpl23, psbZ-trnG-GCC, trnY-GUA-trnE-UUC, trnW-CCA-trnP-UGG, rps16-trnQ-UUG, and psbC-trnS-UGA. The hypervariable coding and noncoding regions in E. maackii were not the same as those in Euonymus. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven Euonymus species formed a clade, which was sister to that formed with Catha edulis and Maytenus guangxiensis, and they separated 24.74 million years ago. E. maackii and E. hamiltonianus were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of E. maackii, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in Euonymus.