Characteristics analysis of the complete Wurfbainia villosa chloroplast genome

Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae

BACKGROUND

The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy.

RESULTS

The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship.

CONCLUSIONS

Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.

Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants

Introduction

The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification.

Methods

In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized.

Results

exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago.

Discussion

The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.

Characterization of the Complete Chloroplast Genome of Four Species in Callerya

BACKGROUND

Callerya reticulata (Bentham) Schot, Callerya dielsiana (Harms) P.K. Loc ex Z. Wei & Pedley, Callerya nitida var. hirsutissima (Z. Wei) X.Y. Zhu, and Callerya nitida (Bentham) R. Geesink, which belongs to the Leguminosae family, are important medicinal plants in China. The genus Callerya includes 26 species, 18 species are distributed in China, and the vine stems of some species are used as traditional medicinal herbs because they have important pharmacological activity. Due to the high similarity of appearance, it is difficult to identify them in the market by appearance alone. Therefore, circulating of Callerya-related materia medica on the market is confusing, sometimes even leading to drug safety problems. It is urgent to develop molecular methods for their identification.

OBJECTIVE

To sequence and analyze the complete chloroplast (cp) genomes of C. reticulata, C. dielsiana, C. nitida var. hirsutissima, and C. nitida and to analyze their cp genome differences as a basis for seeking easier DNA barcoding for their identification.

METHOD

After using Illumina high-throughput sequencing and nanopore sequencing to obtain the genome data, some bioinformatics software was used to assembly and analyze the molecular structure of cp genomes.

RESULTS

The complete cp genomes of the four species were circular molecules, which ranged from 130 435 to 132 546 bp, and GC contents ranged from 33.89% to 34.89%. Each of them includes a large single-copy region, a small single-copy region, and without large inverted repeat regions.

CONCLUSIONS

These results suggested that highly variable regions of the four cp genomes would provide useful plastid markers, which could be used as a potential genomic resource to resolve phylogenetic questions and provide a reference for mining specific DNA barcodes of these species.

HIGHLIGHTS

Our study provided highly effective molecular markers for subsequent phylogenetic analysis, species identification, and biogeographic analysis of Callerya.

TCM-Suite: A comprehensive and holistic platform for Traditional Chinese Medicine component identification and network pharmacology analysis

DNA-based biological ingredient identification and downstream pharmacology network analysis are commonly used in research for Traditional Chinese Medicine preparations (TCM formulas). Advancements in bioinformatics tools and the accumulation of related data have become driving forces for progress in this field. However, a lack of a platform integrating biological ingredient identification and downstream pharmacology network analysis hinders the deep understanding of TCM. In this study, we developed the TCM-Suite platform composed of two sub-databases, Holmes-Suite and Watson-Suite, for TCM biological ingredient identification and network pharmacology investigation, respectively, both are among the most complete: In the Holmes-Suite, we collected and processed six types of marker gene sequences, accounting for 1,251,548 marker gene sequences. In the Watson-Suite, we curated and integrated a massive number of entries from more than 10 public databases. Importantly, we developed a comprehensive pipeline to integrate TCM biological ingredient identification and downstream network pharmacology research, allowing users to simultaneously identify components of a TCM formula and analyze its potential pharmacology mechanism. Furthermore, we designed search engines and a user-friendly platform to better search and visualize these rich resources. TCM-Suite is a comprehensive and holistic platform for TCM-based drug discovery and repurposing. TCM-Suite website: http://TCM-Suite.AImicrobiome.cn.

The complete chloroplast genome sequence of the medicinal plant Abrus pulchellus subsp. cantoniensis: genome structure, comparative and phylogenetic relationship analysis

Abrus pulchellus subsp. cantoniensis, an endemic medicinal plant in southern China, is clinically used to treat jaundice hepatitis, cholecystitis, stomachache and breast carbuncle. Here, we assembled and analyzed the first complete chloroplast (cp) genome of A. pulchellus subsp. cantoniensis. The A. pulchellus subsp. cantoniensis cp genome size is 156,497 bp with 36.5% GC content. The cp genome encodes 130 genes, including 77 protein-coding genes, 30 tRNA genes and four rRNA genes, of which 19 genes are duplicated in the inverted repeats (IR) regions. A total of 30 codons exhibited codon usage bias with A/U-ending. Moreover, 53 putative RNA editing sites were predicted in 20 genes, all of which were cytidine to thymine transitions. Repeat sequence analysis identified 45 repeat structures and 125 simple-sequence repeats (SSRs) in A. pulchellus subsp. cantoniensis cp genome. In addition, 19 mononucleotides (located in atpB, trnV-UAC, ycf3, atpF, rps16, rps18, clpP, rpl16, trnG-UCC and ndhA) and three compound SSRs (located in ndhA, atpB and rpl16) showed species specificity between A. pulchellus subsp. cantoniensis and Abrus precatorius, which might be informative sources for developing molecular markers for species identification. Furthermore, phylogenetic analysis inferred that A. pulchellus subsp. cantoniensis was closely related to A. precatorius, and the genus Abrus formed a subclade with Canavalia in the Millettioid/Phaseoloid clade. These data provide a valuable resource to facilitate the evolutionary relationship and species identification of this species.

Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

BACKGROUND

Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species.

RESULTS

The results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9-37.0%. Gene annotation revealed 106-109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust.

CONCLUSIONS

Our study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.

Estrogenic Plants: to Prevent Neurodegeneration and Memory Loss and Other Symptoms in Women After Menopause

In mammals, sexual hormones such as estrogens play an essential role in maintaining brain homeostasis and function. Estrogen deficit in the brain induces many undesirable symptoms such as learning and memory impairment, sleep and mood disorders, hot flushes, and fatigue. These symptoms are frequent in women who reached menopausal age or have had ovariectomy and in men and women subjected to anti-estrogen therapy. Hormone replacement therapy alleviates menopause symptoms; however, it can increase cardiovascular and cancer diseases. In the search for therapeutic alternatives, medicinal plants and specific synthetic and natural molecules with estrogenic effects have attracted widespread attention between the public and the scientific community. Various plants have been used for centuries to alleviate menstrual and menopause symptoms, such as Cranberry, Ginger, Hops, Milk Thistle, Red clover, Salvia officinalis, Soy, Black cohosh, Turnera diffusa, Ushuva, and Vitex. This review aims to highlight current evidence about estrogenic medicinal plants and their pharmacological effects on cognitive deficits induced by estrogen deficiency during menopause and aging.

The complete chloroplast genome of the rare species Epimedium tianmenshanensis and comparative analysis with related species

Epimedium tianmenshanensis is a rare perennial herb distributed in China, and it is also an important medicinal plant. Here, we used illumina paired-end sequencing technology to obtain the complete chloroplast genome of E. tianmenshanensis, and compared analysis with related species. The length of the complete chloroplast genome of E. tianmenshanensis is 156,956 bp, which is a relatively conserved quadripartite structure including a large single copy (LSC) region of 88,409 bp, a small single copy (SSC) region of 17,448 bp, and a pair of inverted repeat (IRa/IRb) regions of 25,550 bp. The whole genome contains 132 unique genes, including 85 protein-coding genes, 38 tRNA genes, eight rRNA genes and one pseudogene. 87 simple sequence repeats (SSRs) were identified, and most of them were found to be composed of A/T. In addition, 22,923 codons were detected in 78 protein-coding genes of E. tianmenshanensis, and the overall codon bias pattern in the genome tended to use A/U ending codons. Phylogenetic analysis demonstrated that all the Epimedium species formed a monophyletic clade, and E. tianmenshanensis had the closest relationship to E. dolichostemon. The results of this study provided useful molecular information about the evolution and molecular biology of E. tianmenshanensis.