Phylogeny, biogeography, and character evolution of Anaphalis (Gnaphalieae, Asteraceae).

The HAP clade, mainly including Helichrysum Mill, Anaphalis DC., and Pseudognaphalium Kirp., is a major component of tribe Gnaphalieae (Asteraceae). In this clade, Anaphalis represents the largest genus of Asian Gnaphalieae. The intergeneric relationships among Anaphalis and its related genera and the infrageneric taxonomy of this genus are complex and remain controversial. However, there are few studies that have focused on these issues. Herein, based on the current most comprehensive sampling of the HAP clade, especially Anaphalis, we conducted phylogenetic analyses using chloroplast (cp) genome and nuclear ribosomal DNA (nrDNA) to evaluate the relationships within HAP clade, test the monophyly of Anaphalis, and examine the infrageneric taxonomy of this genus. Meanwhile, the morphological characters were verified to determine the circumscription and infrageneric taxonomy system of Anaphalis. Additionally, the biogeographical history, diversification processes, and evolution of crucial morphological characters were estimated and inferred. Our phylogenetic analyses suggested that Anaphalis is polyphyletic because it nested with Helichrysum and Pseudognaphalium. Two and four main clades of Anaphalis were identified in cp genome and nrDNA trees, respectively. Compared with nrDNA trees, the cp genome trees were more effective for phylogenetic resolution. After comprehensively analyzing morphological and phylogenetic evidence, it was concluded that the achene surface ornamentation and leaf base showed less homoplasy and supported the two Anaphalis lineages that were inferred from cp genome. Our biogeographical analyses based on cp genome indicated that HAP clade underwent rapid diversification from late Miocene to Pliocene. The two Anaphalis lineages appeared to have originated in Africa, then spread to Western and Southern Asia, and subsequently moved into Southwestern China forming a diversity center. The dispersal patterns of the two Anaphalis lineages were different. One dispersed around the world, except in Africa and South America. The other one dispersed to Eastern and Southeastern Asia from the ancestral origin region.

High-resolution estimation of near-surface ozone concentration and population exposure risk in China.

Considering the spatial and temporal effects of atmospheric pollutants, using the geographically and temporally weighted regression and geo-intelligent random forest (GTWR-GeoiRF) model and Sentinel-5P satellite remote sensing data, combined with meteorological, emission inventory, site observation, population, elevation, and other data, the high-precision ozone concentration and its spatiotemporal distribution near the ground in China from March 2020 to February 2021 were estimated. On this basis, the pollution status, near-surface ozone concentration, and population exposure risk were analyzed. The findings demonstrate that the estimation outcomes of the GTWR-GeoiRF model have high precision, and the precision of the estimation results is higher compared with that of the non-hybrid model. The downscaling method enhances estimation results to some extent while addressing the issue of limited spatial resolution in some data. China's near-surface ozone concentration distribution in space shows obvious regional and seasonal characteristics. The eastern region has the highest ozone concentrations and the lowest in the northeastern region, and the wintertime low is higher than the summertime high. There are significant differences in ozone population exposure risks, with the highest exposure risks being found in China's eastern region, with population exposure risks mostly ranging from 0.8 to 5.

Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus).

BACKGROUND: Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS: In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS: Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Phylogeny of Trigonotis in China-with a special reference to its nutlet morphology and plastid genome.

The genus Trigonotis comprises nearly 60 species mainly distributed in East and Southeast Asia. China has the largest number of Trigonotis species in the world, with a total of 44 species, of which 38 are endemic. Nutlet morphology is useful for the taxonomic delimitation of Trigonotis. However, there are still controversial circumscriptions of nutlet shape in some species. In previous studies, interspecies phylogenetic relationships were inferred using few DNA markers and very few taxa, which possibly led to erroneous or incomplete conclusions. In this study, the nutlet morphology of 39 Trigonotis taxa and the characteristics of 34 complete chloroplast genomes (29 taxa) were investigated and analyzed. Then, the phylogenetic relationships were discussed within this genus based on complete chloroplast genomes. To the best of our knowledge, this study is the first comprehensive analysis of nutlet morphology and complete chloroplast genome of Trigonotis. Based on nutlet morphology, Trigonotis can be divided into two groups: Group 1, hemispherical or oblique tetrahedron with carpopodiums, and Group 2, inverted tetrahedron without carpopodiums. The chloroplast genome of Trigonotis exhibited a typical quadripartite structure, including 84-86 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes, with a total length of 147,247-148,986 bp. Genes in the junctions were well conserved in Trigonotis, similar to those in other Boraginaceae s.str. species. Furthermore, Trigonotis chloroplast genomes showed relatively high diversity, with more conserved genic regions than intergenic regions; in addition, we detected 14 hot spots (Pi > 0.005) in non-coding regions. Phylogenetic analyses based on chloroplast genome data identified highly resolved relationships between Trigonotis species. Specifically, Trigonotis was divided into two clades with strong support: one clade included species with hemispherical or oblique tetrahedron nutlets with carpopodiums and bracts, whereas the other clade included species with inverted tetrahedron nutlets without carpopodiums or bracts. Our results may inform future taxonomic, phylogenetic, and evolutionary studies on Boraginaceae.

Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA.

The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.

Efficacy and Safety of PRC-063 for Attention-Deficit/Hyperactivity Disorder: A Systematic Review and Meta-analysis From Randomized Controlled Trials.

OBJECTIVE: A new formulation of extended-release methylphenidate (PRC-063) was approved to treat ADHD. This meta-analysis was conducted to study the efficacy and safety of PRC-063 for ADHD. METHOD: We searched for published trials to October 2022 in several databases. RESULTS: A total of 1,215 patients from 5 RCTs were included. We observed significant improvement for PRC-063 in ADHD Rating Scale (ADHD-RS; MD = -6.73, 95% CI [-10.34, -3.12]) compared with placebo. The effect of PRC-063 on the sleep problems due to ADHD was not statistically different from placebo. Six subscales of Pittsburg Sleep Quality Index (PSQI) showed no statistical significance between PRC-063 and placebo. The result showed no significant difference comparing PRC-063 with placebo in serious treatment-emergent adverse events (TEAEs) (RR = 0.80, 95% CI [0.03, 19.34]). In subgroup analysis according to age, PRC-063 was more efficacious in minors compare to adults. CONCLUSION: PRC-063 is an efficacious and safe treatment for ADHD, especially in children and adolescents.

Plastome-based phylogeny and biogeography of Lactuca L. (Asteraceae) support revised lettuce gene pool categories.

This study generated and analyzed complete plastome and internal transcribed spacer (ITS) data of 46 Lactuca species, 13 African endemic (AE) Lactuca species, and 15 species from eight related genera in Lactucinae. The new plastome and nuclear ITS sequences were then used to reconstruct the phylogenetic relationships of Lactuca species. The whole-plastome data were used to estimate divergence time and ancestral area reconstruction of the identified major Lactuca lineages. The results showed that Lactuca species are generally similar in plastome size, Guanine and Cytosine (GC) content, gene structure, and categories, although crop lettuce (Lactuca sativa L.) and its gene pool relatives were found to have one unique pseudogene (ψ ndhF), and accD, atpF, cemA, clpP, and rpl22 showed signs of positive selection. Our phylogenomic analysis demonstrated that Lactuca is monophyletic after excluding Lactuca alatipes Collett and Hemsl and AE Lactuca species. AE Lactuca species are morphologically distinct from core Lactuca lineage and need to be excluded from Lactua. The core Lactuca species most likely originated from Asia-Temperate W ~6.82 Mya and then dispersed globally and formed nine clades. Finally, the lettuce gene pool concept was amended according to the phylogenetic and historical biogeographic analyses. This study revised the circumscription of Lactuca, revealed robust phylogenetic relationships within the genus, and provided insights into Lactucinae phylogeny. The lettuce gene pool species could be used as potential genetic resources for lettuce breeding.

Characterization of the complete chloroplast genome sequence of Isodon japonicus (N. Burman) H. Hara (Lamiaceae).

Isodon japonicus (N. Burman) H. Hara (family: Lamiaceae), is a traditional herbal plant from Henan Province, China. In this study, we sequenced the complete chloroplast genome of I. japonicus sampled from the Funiu Mountains, Henan Province, China. The total length of the chloroplast genome is 152,298 bp, and has a typical quadripartite structure, including a large single-copy region (LSC) of 83,184 bp, a small single-copy region (SSC) of 17,806 bp and a pair of inverted repeats of 25,654 bp. The chloroplast genome of I. japonicus consists of 133 genes, including 88 protein-coding genes, eight rRNA genes, and 37 tRNA genes. There are 34 tandem repeats and 50 simple sequence repeats (SSRs) in the chloroplast genome. The total guanine-cytosine (GC) content of the whole chloroplast genome is 37.6%. Phylogenetic analysis indicated that I. japonicus forms a clade with six other Isodon species and is closely associated with I. rubescens.

Development and characterization of microsatellite markers for Rhododendron purdomii (Ericaceae) using next-generation sequencing.

Rhododendron purdomii (Ericaceae) is an endangered ornamental species endemic to the Qinling Mountains of China. Due to the impact of climate change and human disturbance, R. purdomii is threatened by habitat loss, and conservation of this species is urgently needed. In this study, we developed and characterized 13 novel microsatellite markers for R. purdomii based on next-generation sequencing data. For the 13 microsatellite markers in three R. purdomii populations, the number of alleles ranged from two to 12, the number of effective alleles was from 1.000 to 8.892, Shannon's information index was from 0.000 to 2.320, and the observed and expected heterozygosity were from 0.000 to 1.000 and from 0.000 to 0.888, respectively. Private alleles were found in all three populations. Moderate differentiation between population pairs was indicated by pairwise FST values. The microsatellite markers developed in this study will provide opportunities for examining the genetic diversity and population structure of R. purdomii and contribute to the effective conservation of this species.

Comparative and phylogenetic analyses of Swertia L. (Gentianaceae) medicinal plants (from Qinghai, China) based on complete chloroplast genomes.

Swertia L. is a large genus in Swertiinae (Gentianaceae). In China, many Swertia species are used as traditional Tibetan medicines, known as "Zangyinchen" or "Dida". However, the phylogenetic relationships among Swertia medicinal plants and their wild relatives have remained unclear. In this study, we sequenced and assembled 16 complete chloroplast (cp) genomes of 10 Swertia species, mainly distributed in Qinghai Province, China. The results showed that these species have typical structures and characteristics of plant cp genomes. The sizes of Swertia cp genomes are ranging from 149,488 bp to 154,097 bp. Most Swertia cp genomes presented 134 genes, including 85 protein coding genes, eight rRNA genes, 37 tRNA genes, and four pseudogenes. Furthermore, the GC contents and boundaries of cp genomes are similar among Swertia species. The phylogenetic analyses indicated that Swertia is a complex polyphyletic group. In addition, positive selection was found in psaI and petL genes, indicating the possible adaptation of Qinghai Swertia species to the light environment of the Qinghai-Tibet plateau. These new cp genome data could be further investigated to develop DNA barcodes for Swertia medicinal plants and for additional systematic studies of Swertia and Swertiinae species.

Development of polymorphic microsatellite markers for the Tertiary relict tree species Taiwania cryptomerioides (Cupressaceae) in East Asia.

Taiwania cryptomerioides Hayata is an endangered relict tree species which is endemic to mainland China, Taiwan, Myanmar, and northern Vietnam. It is an economically important tree species and has been used for reforestation in mountain areas of mainland China and Taiwan. In order to investigate its genetic diversity for conservation and restoration, we developed and characterized 15 nuclear microsatellite markers based on next-generation sequencing data. A total of 100 microsatellite primer pairs were initially designed and tested based on the restriction-site associated DNA sequencing data. 60 of 100 loci (60%) were successfully amplified, of which 42 loci exhibited polymorphism. Fifteen polymorphic microsatellite loci with clear peaks were selected for further analyses in four T. cryptomerioides populations sampled from China (Hubei, Fujian, Guizhou, and Yunnan). The number of alleles per locus ranged from 2 to 24, and the levels of observed and expected heterozygosity ranged from 0.000 to 0.950 and from 0.000 to 0.860, respectively. This set of microsatellite markers will be useful for future population genetic studies of T. cryptomerioides in East Asia.

The complete mitochondrial genome of a Chinese endemic species, Paraprenanthes diversifolia (Vaniot) N. Kilian (Cichorieae; Asteraceae).

The first complete mitochondrial genome (mt) of Paraprenanthes diversifolia (Vaniot) N. Kilian (Cichorieae; Asteraceae) was sequenced and successfully assembled in this study. The full length of the mt genome is 360,751 bp, containing 73 genes (33 protein-coding genes, 29 tRNA genes, 6 rRNA genes, and 5 protein-coding genes containing internal stop codons). There are two pairs of long (over 1000 bp) repeat regions in the mt genome of P. diversifolia. The phylogenetic analysis indicated that P. diversifolia has a close relationship with other Lactucinae species.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine.

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

[Early changes in renal injury parameters and their influencing factors in workers exposed to mercury].

OBJECTIVE: To investigate atmospheric mercury concentration in the workplace and urinary mercury concentration in workers exposed to mercury in a thermometer factory, and to determine the levels and influencing factors of urinary Β2-microglobulin (Β2-MG) and retinol-binding protein (RBP) in these workers. METHODS: An occupational health survey of the workplace was completed according to relevant national occupational health standards. Questionnaire survey and occupational health examination were conducted in 178 workers exposed to mercury in the factory. Statistical analysis was accomplished using SPSS 19.0. RESULTS: In the workplace, atmospheric mercury concentration was out of limits at seven of eight detection points expressed by short-term exposure limit; it was out of limits at all the eight detection points shown by time-weighted average. Statistically significant difference in atmospheric mercury concentration was found among different detection points (F = 138.714, P < 0.001). The geometric mean of urinary mercury concentration measured in 154 workers was 171.607 µg/g. There were 127 workers with urinary mercury concentration exceeding the standard (82.5% over-standard rate). Significant difference in urinary mercury concentration was shown in the workers among different positions (χ² = 44.531, P < 0.01). Urinary mercury concentration was positively correlated with atmospheric mercury concentration (r = 0.624, P < 0.01). The mean urinary Β2-MG level measured in 148 workers was 0.142 mg/L, and seven workers had urinary Β2-MG levels greater than 0.3 mg/L (4.7% abnormal rate). The mean urinary RBP level measured in 153 workers was 0.485 mg/L, and 19 workers had urinary RBP levels greater than 0.7 mg/L (12.4% abnormal rate). Ordinal logistic regression showed that age >34 years (OR = 4.88, 95%CI: 2.24∼10.62) and length of service >15 years (OR = 2.50, 95%CI: 1.06-5.92) were risk factors for increased urinary Β2-MG level. Age >45 years (OR = 7.52, 95%CI: 2.50∼22.65) was a risk factor for increased urinary RBP level. CONCLUSION: In the thermometer factory under study, atmospheric and urinary mercury concentrations both seriously exceeded the standards, which were harmful to the health of workers. High atmospheric mercury concentration, old age, and long length of service were risk factors for increased urinary Β2-MG and RBP levels in workers exposed to mercury.