Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family.

Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include economically important species, such as cacao, cotton, durian, and jute, with cotton an important model system for studying the domestication of polyploids. Here, we use chromosome-level genome assemblies from representatives of five or six subfamilies (depending on the placement of Ochroma) to differentiate coexisting subgenomes and their evolution during the family's deep history. The results reveal that the allohexaploid Helicteroideae partially derive from an allotetraploid Sterculioideae and also form a component of the allodecaploid Bombacoideae and Malvoideae. The ancestral Malvaceae karyotype consists of 11 protochromosomes. Four subfamilies share a unique reciprocal chromosome translocation, and two other subfamilies share a chromosome fusion. DNA alignments of single-copy nuclear genes do not yield the same relationships as inferred from chromosome structural traits, probably because of genes originating from different ancestral subgenomes. These results illustrate how chromosome-structural data can unravel the evolutionary history of groups with ancient hybrid genomes.

Simultaneous determination of four phytoecdysteroids by LC-MS/MS: application to a comparative pharmacokinetic study in normal and adjuvant arthritis rats after oral administration of C. officinalis Kuan phytoecdysteroids extract.

C. officinalis Kuan is the dry root of Cyathula officinalis Kuan. Clinically, it is used for fall and flutter injury, rheumatism and arthralgia. Phytoecdysteroids have significant anti-inflammatory effects, and the phytoecdysteroids present in C. officinalis Kuan exhibit potential for treating rheumatoid arthritis.This study first developed a selective, accurate and efficient LC-MS/MS method for 12-day pharmacokinetic studies regarding the simultaneous determination of cyasterone, 25-epi-28-epi-cyasterone, precyasterone and capitasterone from C. officinalis Kuan phytoecdysteroids extract in normal and adjuvant arthritis rats.An Agilent Eclipse Plus C18 RRHD column (1.8 µm, 50mm × 2.1 mm) with a gradient mobile phase consisting of water (A) and acetonitrile (B) was used for analysis. The mass analysis was performed in an Agilent 6430 QQQ-MS mass spectrometer with positive mode multiple reaction monitoring (MRM).The results indicated that the AUC0-t and AUC0-∞ values of the four phytoecdysteroids in adjuvant arthritis rats were different from those in normal rats on the first day, which could provide a helpful reference for pharmacological and toxicological studies, as well as clinical applications of C. officinalis Kuan in the treatment of rheumatoid arthritis.

1. C. officinalis Kuan is the dry root of Cyathula officinalis Kuan which has been used for the treatment of flapping injury, rheumatism arthralgia, foot flaccidity, and tendon contracture thousands of years in China, and has been officially included in the Chinese Pharmacopoeia.2. A highly accurate, stable, and sensitive ultra-performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) method was first established and validated for simultaneously determination four phytoecdysteroids: cyasterone, 25-epi-28-epi-cyasterone, precyasterone and capitasterone in normal and adjuvant arthritis rats plasma samples 12 days of continuous gavage of C. officinalis Kuan phytoecdysteroids extract.3. The phytoecdysteroids is the important component of C. officinalis Kuan, which is difficult to separated. And there is no report for the pharmacokinetic study of phytoecdysteroids from C. officinalis Kuan. And the method provides a good reference for the follow-up studies clinical medication of the phytoecdysteroids from C. officinalis Kuan.

Simultaneous determination and pharmacokinetics study of three triterpenoid saponins in rat plasma by ultra-high-performance liquid chromatography tandem mass-spectrometry after oral administration of Astragalus Membranaceus leaf extract.

A selective and sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry method was developed and validated for the determination of three triterpenoid saponins isolated from Astragalus membranaceus leaf extract. In this article, a method for simultaneous determination of Huangqiyenin A, Huangqiyenin E, and Huangqiyenin K was established for the first time. The method was successfully applied to the pharmacokinetic study of Astragalus membranaceus leaf extract after oral administration. Liquid-liquid extraction was applied to plasma sample preparation. Multiple reaction monitoring mode with an electrospray ion source in positive electrospray ionization was chosen to quantify the analytes. Chromatographic separation was performed on a Waters HSS T3 column, using gradient elution with a mobile phase composed of acetonitrile and 5 mM ammonium acetate/water. The pharmacokinetic results showed that all three compounds had the characteristics of rapid absorption-slow metabolism trend. The time of maximum plasma concentration of Huangqiyenin A is higher than Huangqiyenin E and Huangqiyenin K. And the maximum plasma concentration of Huangqiyenin A is higher as well. The pharmacokinetic results revealed the pharmacokinetic characteristics of the three analytes in rat plasma, which could provide a helpful reference for the further study of Astragalus membranaceus leaf extract.

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis.

Rhubarb is the collective name for various perennial plants from the genus Rheum L. and the Polygonaceae family. They are one of the most ancient, commonly used, and important herbs in traditional Chinese medicine. Rhubarb is a major source of anthraquinones, but how they are synthesized remains largely unknown. Here, we generate a genome sequence assembly of one important medicinal rhubarb R. tanguticum at the chromosome level, with 2.76 Gb assembled into 11 chromosomes. The genome is shaped by two recent whole-genome duplication events and recent bursts of retrotransposons. Metabolic analyses show that the major anthraquinones are mainly synthesized in its roots. Transcriptomic analysis reveals a co-expression module with a high correlation to anthraquinone biosynthesis that includes key chalcone synthase genes. One CHS, four CYP450 and two BGL genes involved in secondary metabolism show significantly upregulated expression levels in roots compared with other tissues and clustered in the co-expression module, which implies that they may also act as candidate genes for anthraquinone biosynthesis. This study provides valuable insights into the genetic bases of anthraquinone biosynthesis that will facilitate improved breeding practices and agronomic properties for rhubarb in the future.

Simultaneous Determination of Five Iridoids of Picrorhiza scrophulariiflora in Rat Plasma Using UHPLC-ESI-MS/MS.

In this study, we developed an ultra-performance liquid chromatography-electrospray tandem quadrupole mass spectrometry (UHPLC-ESI-MS/MS) method to simultaneously determine Picroside-I, Picroside-II, Picroside-III, minecoside, and sweroside in rat plasma. The chromatographic column was an ACQUITY UHPLC® BEH Amide Column (2.1 × 100 mm, 1.7 µm; Waters, MA, USA), column temperature 40 °C. The mobile phase was 0.1% formic acid aqueous solution-0.1% formic acid acetonitrile solution. The flow rate was 0.4 mL/min. Multiple reaction monitoring (MRM) and negative ion modes were adopted. The results showed that the calibration curves of five compounds in plasma showed good linearity (r > 0.9911) over the studied dose range. The lower limits of quantification (LLOQ) for Picroside-I, Picroside-II, Picroside-III, minecoside, and sweroside were 6.876, 5.193, 5.040, 1.260, and 4.527 ng/mL, respectively. The intra-day and inter-day precision were <15%. The matrix effects ranged from 95.77 to 101.9%. The Tmax were 1.1 ± 0.2, 1.1 ± 0.1, 0.8 ± 0.1, 1.0 ± 0.2, and 2.1 ± 0.1 h. This study will be useful in understanding the behavior of drugs in the body and the body's effect on drugs. It also offers theoretical underpinnings and highlights the importance of clinical applications and creating novel drugs.

Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau.

Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. Numerous genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.

An ultra-high-performance liquid chromatography-tandem mass spectrometry method for the simultaneous quantitation of 10 alkaloids of Corydalis Decumbentis Rhizoma preparation in dog plasma and its application to a pharmacokinetic study.

OBJECTIVE: A sensitive and rapid ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was successfully applied to the determination of 10 alkaloids in beagle dog plasma following a single oral dose of Xiatianwu capsules and enteric-coated capsules, with theophylline serving as the internal standard (IS). METHODS: Plasma samples were preprocessed using liquid-liquid extraction (LLE) with ethyl acetate ahead to separation using a gradient elution procedure on a Waters ACQUITY UPLC HSS T3 column (1.8 µm, 100 × 2.1 mm). The mobile phase was composed of 0.1% formic acid solution and acetonitrile at the flow rate of 0.3 ml/min. Multiple reaction monitoring (MRM) was used to determine the analytes in the positive ion mode. RESULTS: The calibration curves for 10 analytes demonstrated a high degree of linearity (r ≥ 0.9920). The lower limit of quantification (LLOQ) values for 10 alkaloids were all more than 1.074 ng/ml, and matrix effects varied from 94.25% to 106.15%. The mean extraction recovery of quality control samples at low (LQC), medium (MQC) and high (HQC) concentrations, as well as IS, was all more than 76.60%. The intra-day and inter-day precision (RSD) also satisfied the requirement. Simultaneously, the variation of assay accuracies (RE) was between 13.05% and 9.38%. CONCLUSION: The test was validated in accordance with regulatory bioanalytical guidelines and was found to be suitable for use in a pharmacokinetic investigation of these compounds in beagle dogs after oral administration of Xiatianwu general capsules and enteric-coated capsules. The Cmax of 10 alkaloids ranged from 52.61 to 192.46 ng/ml after oral administration of Xiatianwu capsules, and from 67.50 to 247.36 ng/ml. The Tmax was between 0.59 and 1.33 h of Xiatianwu capsules, and between 1.08 and 2.00 h of enteric-coated capsules. The t1/2 ranged from 3.18 to 7.47 h of general capsules, and from 6.01 to 11.36 h. AUC0-t ranged from 181.06 to 722.74 ng·h/ml of Xiatianwu capsules, and from 275.03 to 884.17 ng·h/ml of enteric-coated capsules. The Cmax of enteric-coated capsules were significantly increased except for tetrahydropalmatine and berberine. Tmax of general capsules were less than 1 h, and of enteric-coated capsules were less than 2 h. The t1/2 of dehydrocorydaline, palmatine, tetrahydrojatrorrhizine, jatrorrhizine and coptisine in enteric-coated capsules was longer than that in ordinary capsule. The AUC0-t and AUC0-∞ of bicuculline, dehydrocorydaline, protopine, magnoflorine, tetrahydrojatrorrhizine, jatrorrhizine, berberine and coptisine were all significantly higher in enteric-coated capsules.

Variation of Saponins in Sanguisorba officinalis L. before and after Processing (Paozhi) and Its Effects on Colon Cancer Cells In Vitro.

The incidence of colon cancer is increasing year over year, seriously affecting human health and quality of life in recent years. However, traditional Chinese medicine (TCM) has been utilized for the treatment of colon cancer. S. officinalis Saponins (S-Saponins), the potential compound of TCM, displays multiple biological activities in colon cancer treatment. In our study, ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) combined with multivariate statistical analysis were performed to analyze and identify raw and processed saponins. Then, MTT and cell migration assays were used to preliminarily explore the effects of saponins in vitro on colon cancer cells. The results showed that 29 differential saponins compounds under Paozhi were identified by UHPLC-MS/MS. Moreover, in vitro validation showed that Sprocessed better inhibited the proliferation and migration of colon cancer cells than Sraw. This study provides a basis for the determination of the chemical fundamentals of the efficacy changes during Paozhi through inferring the changes in saponin components and its possible transformation mechanisms before and after processing S. officinalis. Meanwhile, it also provides new insights into potential bioactive ingredients for the treatment of colon cancer.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots.

BACKGROUND: Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. RESULTS: Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. CONCLUSIONS: Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots.

Simultaneous Determination and Pharmacokinetics Study of Three Triterpenes from Sanguisorba officinalis L. in Rats by UHPLC-MS/MS.

A selective and rapid ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was established and validated for the determination of ziyuglycoside I, 3ß,19α-dihydroxyurs-12-en-28-oic-acid 28-ß-d-glucopyranosyl ester, and pomolic acid in rats after the oral administration of ziyuglycoside I, 3ß,19α-dihydroxyurs-12-en-28-oic-acid 28-ß-d-glucopyranosyl ester, pomolic acid, and Sanguisorba officinalis L. extract. The separation was carried out on an ACQUITY UPLC®HSS T3 column (2.1 mm × 100 mm, 1.8 µm), using methanol and 5 mmol/L ammonium acetate water as the mobile phase. The three compounds were quantified using the multiple reaction monitoring mode with the electrospray ion source in both the positive and negative mode. Liquid-liquid extraction was applied to the plasma sample preparation. Bifendate was selected as the internal standard. The intra-day and inter-day precision and the accuracy of the method were all within receivable ranges. The lower limit of quantification of ziyuglycoside I, 3ß,19α-dihydroxyurs-12-en-28-oic-acid 28-ß-d-glucopyranosyl ester, and pomolic acid were 6.50, 5.75, and 2.63 ng/mL, respectively. The extraction recoveries of analytes in rat plasma ranged from 83 to 94%. The three components could be rapidly absorbed into the blood (Tmax, 1.4-1.6 h) both in the single-administration group or S. officinalis extract group, but the first peak of PA occurred at 0.5 h and the second peak at 4-5 h in the S. officinalis extract. Three compounds were eliminated relatively slowly (t1/2, 7.3-11 h). The research was to establish a rapid, sensible, and sensitive UHPLC-MS/MS method using the multi-ion mode for multi-channel simultaneous mensuration pharmacokinetics parameters of three compounds in rats after oral administration of S. officinalis extract. This study found, for the first time, differences in the pharmacokinetic parameters of the three compounds in the monomer compounds and S. officinalis extract administration, which preliminarily revealed the transformation and metabolism of the three compounds in vivo.

Transcriptomic analysis reveals the mechanism of host growth promotion by endophytic fungus of Rumex gmelinii Turcz.

Rumex gmelinii Turcz. (RGT) is a medicinal plant of the genus Rumex, family Polygonaceae. Our research group isolated an endophytic fungus, Plectosphaerella cucumerina (Strain J-G) from RGT, which could significantly promote host growth when co-cultured with host seedlings. In this study, we used transcriptome analysis and verification experiments to explore the molecular mechanisms underlying this growth-promoting effect. We found that, during co-culture with Strain J-G, the expression of genes encoding key enzymes in amino acid metabolism and carbohydrate synthesis and metabolism were up-regulated in RGT tissue culture seedlings, providing additional substrate and energy for plant growth. In addition, the expression of genes encoding the responser of RGT seedlings to hormones, including auxin and cytokinin, were significantly enhanced, promoting plant growth and development. Furthermore, RGT seedling defense systems were mobilized by Strain J-G; therefore, more secondary metabolites and substances involved in stress resistance were produced, ensuring normal plant growth and metabolism. The research showed Strain J-G significantly promote the accumulation of biomass and effective components of RGT, which provide basis for its application. This research also provides a reference method for the study of growth-promoting mechanism of endophytic fungi.

Identification of FtpA, a Dps-Like Protein Involved in Anti-Oxidative Stress and Virulence in Actinobacillus pleuropneumoniae.

Bacteria have evolved a variety of enzymes to eliminate endogenous or host-derived oxidative stress factors. The Dps protein, first identified in Escherichia coli, contains a ferroxidase center, and protects bacteria from reactive oxygen species damage. Little is known of the role of Dps-like proteins in bacterial pathogenesis. Actinobacillus pleuropneumoniae causes pleuropneumonia, a respiratory disease of swine. The A. pleuropneumoniae ftpA gene is upregulated during shifts to anaerobiosis, in biofilms and, as found in this study, in the presence of H2O2. An A. pleuropneumoniae ftpA deletion mutant (ΔftpA) had increased H2O2 sensitivity, decreased intracellular viability in macrophages, and decreased virulence in a mouse infection model. Expression of ftpA in an E. coli dps mutant restored wild-type H2O2 resistance. FtpA possesses a conserved ferritin domain containing a ferroxidase site. Recombinant rFtpA bound and oxidized Fe2+ reversibly. Under aerobic conditions, the viability of an ΔftpA mutant was reduced compared with the wild-type strain after extended culture, upon transition from anaerobic to aerobic conditions, and upon supplementation with Fenton reaction substrates. Under anaerobic conditions, the addition of H2O2 resulted in a more severe growth defect of ΔftpA than it did under aerobic conditions. Therefore, by oxidizing and mineralizing Fe2+, FtpA alleviates the oxidative damage mediated by intracellular Fenton reactions. Furthermore, by mutational analysis, two residues were confirmed to be critical for Fe2+ binding and oxidization, as well as for A. pleuropneumoniae H2O2 resistance. Taken together, the results of this study demonstrate that A. pleuropneumoniae FtpA is a Dps-like protein, playing critical roles in oxidative stress resistance and virulence. IMPORTANCE As a ferroxidase, Dps of Escherichia coli can protect bacteria from reactive oxygen species damage, but its role in bacterial pathogenesis has received little attention. In this study, FtpA of the swine respiratory pathogen A. pleuropneumoniae was identified as a new Dps-like protein. It facilitated A. pleuropneumoniae resistance to H2O2, survival in macrophages, and infection in vivo. FtpA could bind and oxidize Fe2+ through two important residues in its ferroxidase site and protected the bacteria from oxidative damage mediated by the intracellular Fenton reaction. These findings provide new insights into the role of the FtpA-based antioxidant system in the pathogenesis of A. pleuropneumoniae, and the conserved Fe2+ binding ligands in Dps/FtpA provide novel drug target candidates for disease prevention.

The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms.

Most extant angiosperms belong to Mesangiospermae, which comprises eudicots, monocots, magnoliids, Chloranthales and Ceratophyllales. However, phylogenetic relationships between these five lineages remain unclear. Here, we report the high-quality genome of a member of the Chloranthales lineage (Chloranthus sessilifolius). We detect only one whole genome duplication within this species and find that polyploidization events in different Mesangiospermae lineage are mutually independent. We also find that the members of all floral development-related gene lineages are present in C. sessilifolius despite its extremely simplified flower. The AP1 and PI genes, however, show a weak floral tissue-specialized expression. Our phylogenomic analyses suggest that Chloranthales and magnoliids are sister groups, and both are together sister to the clade comprising Ceratophyllales and eudicots, while the monocot lineage is sister to all other Mesangiospermae. Our findings suggest that in addition to hybridization, incomplete lineage sorting may largely account for phylogenetic inconsistencies between the observed gene trees.

Clinical efficacy of repeated intra-articular pulsed radiofrequency for the treatment of knee joint pain and its effects on inflammatory cytokines in synovial fluid of patients.

The application value of repeated intra-articular pulsed radiofrequency for the treatment of knee joint pain has remained to be determined. To investigate this, a total of 64 patients with chronic knee joint pain admitted to Caoxian People's Hospital (Caoxian, Chine) between October 2016 and May 2018 were enrolled in the present study and analyzed prospectively. The patients were randomly divided into a control group, receiving treatment with a single intra-articular pulsed radiofrequency through the knee joint (n=32), and an experimental group, receiving multiple intra-articular pulsed radiofrequency treatments through the knee joint (n=32). The visual analog scale score (VAS), clinical efficacy and adverse reactions prior to and after treatment were compared between the two treatments. Synovial fluid cytokines were measured using ELISA prior to and after treatment. After the treatment, the control group and the experimental group both had a lower VAS (P<0.001) and the control group had a higher VAS and lower pain relief than the experimental group (P<0.001). The control group had a total effectiveness rate of 78.13%, with 13 patients experiencing complete relief (40.63%), 12 patients exhibiting a marked improvement (37.5%) and 7 patients reporting no effects (21.87%). The experimental group had a total effectiveness rate of 90.63%, with 18 patients (56.25%) being cured, 11 patients having a marked effect (34.37%) and 3 patients reporting no effects (9.38%). The experimental group had a higher incidence of adverse reactions than the control group (P<0.05). After treatment, the two groups had decreased IL-6, IL-10 and TNF-α levels in the knee joint synovial fluid (P<0.05), with the experimental group having lower cytokine levels than the control group (P<0.05). These results indicated that repeated intra-articular pulsed radiofrequency is an effective method for the treatment of knee joint pain and may be used in clinical practice.

Determination of Triterpenoids and Phenolic Acids from Sanguisorba officinalis L. by HPLC-ELSD and Its Application.

A novel analytical method involving high-performance liquid chromatography with evaporative light scattering detection (HPLC-ELSD) was developed for simultaneous determination of 11 phenolic acids and 12 triterpenes in Sanguisorba officinalis L. Chromatographic separation was conducted with gradient elution mode by using a DiamonsilTM C18 column (250 mm × 4.6 mm, 5 µm) with the mobile phase of 0.1% acetic acid water (A) and methanol (B). The drift tube temperature of ELSD was set at 70 °C and the nitrogen cumulative flow rate was 1.6 L/min. The method was fully validated to be linear over a wide concentration range (R2 ≥ 0.9991). The precisions (RSD) were less than 3.0% and the recoveries were between 97.7% and 101.4% for all compounds. The results indicated that this method is accurate and effective for the determination of 23 functional components in Sanguisorba officinalis L. and could also be successfully applied to study the influence of processing method on those functional components in Sanguisorba officinalis L.

Functional identification and characterization of GST genes in the Asian gypsy moth in response to poplar secondary metabolites.

The Asian gypsy moth, Lymantria dispar, as one of the most important forest pests in the world, can feed on more than 500 species of host plants, causing serious damage to the forests. Poplar is one of the favorite host plants of L. dispar. The present study aimed to explore the effects of poplar secondary metabolites on the growth and detoxification function of L. dispar larvae. We also aimed to study the expression of glutathione S-transferase (GST) genes in different developmental stages and in response to treatment with secondary metabolites. Six kinds of main secondary metabolites and three groups of characteristic mixed secondary metabolites were selected as follows: Caffeic acid, salicin, rutin, quercetin, catechol, flavone, mixture 1 (salicin and flavone), mixture 2 (salicin, caffeic acid and catechol), and mixture 3 (flavone, caffeic acid and catechol) according to the content changes of secondary metabolites in poplar. The thirteen GST genes were selected as candidate genes to study the expression of GST genes in different developmental stages and after treatment with secondary metabolites using quantitative real-time reverse transcription PCR. The LdGSTe4 and LdGSTo1 genes could be induced by secondary metabolites and were screened to explore their detoxification function against secondary metabolites using RNA interference technology. The results showed that salicin and rutin significantly induced the expression of LdGSTe4 and LdGSTo1. Under the stress of secondary metabolites, LdGSTe4 silencing affected the adaptability of L. dispar larvae to salicin and rutin. LdGSTe4 silencing resulted in a significant decrease in the body weight of L. dispar, but had little effect on the relative growth rate, relative consumption rate, efficiency of conversion of ingested food, efficiency of conversion of digested food, and approximate digestibility, as well as the survival rate and development time. These results provide a deeper understanding of the adaptive mechanism of L. dispar to host plants, form the foundation for the further research into the host resistance mechanism, and identify target genes for breeding resistant transgenic poplar.

The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding.

Hazelnut is popular for its flavor, and it has also been suggested that hazelnut is beneficial to cardiovascular health because it is rich in oleic acid. Here, we report the first high-quality chromosome-scale genome for the hazelnut species Corylus mandshurica (2n = 22), which has a high concentration of oleic acid in its nuts. The assembled genome is 367.67 Mb in length, and the contig N50 is 14.85 Mb. All contigs were assembled into 11 chromosomes, and 28,409 protein-coding genes were annotated. We reconstructed the evolutionary trajectories of the genomes of Betulaceae species and revealed that the 11 chromosomes of the hazelnut genus were derived from the most ancestral karyotype in Betula pendula, which has 14 protochromosomes, by inferring homology among five Betulaceae genomes. We identified 96 candidate genes involved in oleic acid biosynthesis, and 10 showed rapid evolution or positive selection. These findings will help us to understand the mechanisms of lipid synthesis and storage in hazelnuts. Several gene families related to salicylic acid metabolism and stress responses experienced rapid expansion in this hazelnut species, which may have increased its stress tolerance. The reference genome presented here constitutes a valuable resource for molecular breeding and genetic improvement of the important agronomic properties of hazelnut.

Which factors contribute most to genome size variation within angiosperms?

Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It has been reported that many factors correlate with the variation in genome size, but few studies have systematically explored this at the genomic level. Here, we scan genomic information for 74 species from 74 families in 38 orders covering the major groups of angiosperms (the taxonomic information was acquired from the latest Angiosperm Phylogeny Group (APG IV) system) to evaluate the correlation between genome size variation and different genome characteristics: polyploidization, different types of repeat sequence content, and the dynamics of long terminal repeat retrotransposons (LTRs). Surprisingly, we found that polyploidization shows no significant correlation with genome size, while LTR content demonstrates a significantly positive correlation. This may be due to genome instability after polyploidization, and since LTRs occupy most of the genome content, it may directly result in most of the genome variation. We found that the LTR insertion time is significantly negatively correlated with genome size, which may reflect the competition between insertion and deletion of LTRs in each genome, and that the old insertions are usually easy to recognize and eliminate. We also noticed that most of the LTR burst occurred within the last 3 million years, a timeframe consistent with the violent climate fluctuations in the Pleistocene. Our findings enhance our understanding of genome size evolution within angiosperms, and our methods offer immediate implications for corresponding research in other datasets.

Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history.

Medicago ruthenica has been recently cultivated as a new forage crop and has been recognized as a source of genes to improve abiotic stress tolerance in cultivated alfalfa because of its remarkable tolerance to drought, salinity-alkalinity, and cold and snowy winters. Here, we reveal a chromosome-scale genome sequence of M. ruthenica based on Illumina, PacBio, and Hi-C data. The assembled genome consists of 903.56 Mb with 50,268 annotated protein-coding genes, which is larger and contains relatively more genes than Medicago truncatula (420 Mb and 44,623 genes) and Medicago sativa spp. caerulea (793 Mb and 47,202 genes). All three species shared the ancestral Papilionoideae whole-genome duplication event before their divergence. The more recent expansion of repetitive elements compared to that in the other two species was determined to have contributed greatly to the larger genome size of M. ruthenica. We further found that multiple gene and transcription factor families (e.g., SOS homologous genes, NAC, C2H2, and CAMTA) have expanded in M. ruthenica, which might have led to its enhanced tolerance to abiotic stress. In addition, M. ruthenica harbors more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed two genetic lineages, reflecting the west and east of its geographical distribution, respectively. The two lineages probably diverged during the last glaciation and survived in multiple refugia at the last glacial maximum, followed by recent expansion. Our genomic data provide a genetic basis for further molecular breeding research on M. ruthenica and alfalfa.