Species diversity and taxonomy of Vararia (Russulales, Basidiomycota) with descriptions of six species from Southwestern China.

Vararia is a species-rich genus in the family Peniophoraceae and has been shown to be polyphyletic. In this study, sequences of ITS and LSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed with the maximum likelihood, maximum parsimony, and Bayesian inference methods. Seventeen lineages including six new species from China, i.e., V.fissurata, V.lincangensis, V.punctata, V.isabellina, V.sinensis, and V.yaoshanensis were recognized, in which V.fissurata is characterized by the brittle basidiomata with pruinose and cracking hymenophore having white to olivaceous buff hymenial surface, the clamped generative hyphae, presence of the two types gloeocystidia; V.lincangensis is characterized by the simple-septa generative hyphae, and thick-walled skeletal hyphae, and ellipsoid basidiospores; V.punctata is delimited by its thin to slightly thick-walled generative hyphae, and thick-walled skeletal hyphae, present thick-walled, clavate to cylindrical gloeocystidia; V.isabellina is characterized by having the cream to isabelline to slightly brown hymenial surface, thin to slightly thick-walled generative hyphae, and sub-fusiform to navicular basidiospores; V.sinensis is distinguishable by its white to slightly pink hymenial surface, thick-walled skeletal hyphae, and sub-fusiform to navicular basidiospores; V.yaoshanensis is characterized by cream to pinkish buff to cinnamon-buff hymenial surface, slightly thick-walled generative hyphae, the presence of two types gloeocystidia, and slightly thick-walled, ellipsoid basidiospores. Phylogram based on the ITS+nLSU rDNA gene regions included nine genera within the family Peniophoraceae as Amylostereum, Asterostroma, Baltazaria, Dichostereum, Michenera, Peniophora, Scytinostroma and Vararia, in which the six new wood-inhabiting fungi species were grouped into genus Vararia. The phylogenetic tree inferred from the combined ITS and LSU tree sequences highlighted that V.fissurata was found to be the sister to V.ellipsospora with strong supports. Additionally, V.lincangensis was clustered with V.fragilis. Furthermore, V.punctata was retrieved as a sister to V.ambigua. Moreover, V.sinensis was grouped with five taxa as V.breviphysa, V.pirispora, V.fusispora, V.abortiphysa and V.insolita. The new species V.isabellina formed a monophyletic lineage, in which it was then grouped closely with V.daweishanensis, and V.gracilispora. In addition, V.yaoshanensis was found to be the sister to V.gallica with strong supports. The present results increased the knowledge of Vararia species diversity and taxonomy of corticioid fungi in China. An identification key to 17 species of Vararia in China is provided.

The complete chloroplast genomes of three Alismataceae species, including the medicinally important Alisma orientale.

Alismataceae is one of the early diverged families of monocotyledonous plants. We report the complete chloroplast genomes of three Alisma species, including Alisma orientale (Sam.) Juzep. 1934, A. subcordatum Raf. 1908, and A. triviale Pursh 1813, of which A. orientale is a traditional Chinese medical plant used widely to treat diuretics, diabetes, hepatitis, and inflammation. We sequenced the complete chloroplast genomes with the Illumina Nova-Seq 6000 platform using herbarium collections. The chloroplast genomes of A. orientale, A. subcordatum and A. triviale are 159,861 bp, 160,180 bp, and 159,727 bp in length, respectively. The three chloroplast genomes each contain 113 genes, including four rRNAs, 30 tRNAs genes, and 79 protein-coding genes, and the average GC content is 36.0%. Based on the whole chloroplast genomes of 19 species of Alismataceae and the close allies, the medicinally important A. orientale was found to be closely related to another medicinal plant Alisma plantago-aquatica L. 1753 in the phylogenetic analysis. The genus Alisma was supported to be monophyletic.

Botany and geogenomics: Constraining geological hypotheses in the neotropics with large-scale genetic data derived from plants.

Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.

The role of climatic variables on nest evolution in tanagers.

Avian nests are fundamental structures in avian reproduction and face strong selective forces. Climatic conditions are likely to have shaped the evolution of specific nest traits, but evidence is scarce at a macroevolutionary level. The Thraupidae family (commonly known as tanagers) is an ideal clade to understand the link between nest architecture and climate because it presents wide variation in nest traits. To understand whether climatic variables have played a role in the diversification of nest traits among species in this family, we measured nests from 49 species using museum collections. We observed that dome-nesting species are present in dryer and hotter environments, in line with previous findings suggesting that domed nests are a specialisation for arid conditions. We also found evidence that nests with thicker walls are present in locations with lower precipitation and that solar radiation can influence the shape of domed nests; birds tend to build shorter and narrower domes in areas with high levels of solar radiation. Open nest architecture is also potentially influenced by wind speed, with longer and deeper nests in areas characterised by strong winds. Our results support the hypothesis that different climatic variables can drive the evolution of specific aspects of nest architecture and contribute to the diversity of nest shapes we currently observe. However, climatic variables account only for a small fraction of the observed structural variation, leaving a significant portion still unexplained.

Vertical Transmission of Hepatitis C Virus Among Women with a History of Injection Opioid Use.

We evaluated vertical transmission and linkage to care in women with HCV and history of injection drug use employing co-localized testing and treatment. Transmission occurred in 1 of 23 infants, with mother-infant genetic distance of 1.26%. Rates for infant testing, maternal linkage and cure were 77%, 52%, and 100%, respectively.

Molecular detection and identification of Plasmodium spp. isolated from captive-bred cynomolgus monkeys in Bogor, Indonesia.

Background and Aim: Asian macaques are natural hosts of several Plasmodium species. Some monkey malaria parasites may infect humans and cause zoonotic infections. This study was conducted to estimate the prevalence of monkey malaria parasites in Bogor, Indonesia, based on molecular detection and identification, particularly in cynomolgus monkeys, which have a wide geographic distribution and share extensive habitats with humans. These data are needed to evaluate the status of simian malaria among macaques in Bogor and to study the potential risks to human health. These updated data will provide sufficient information for implementing malaria control strategies in the future and for developing a potential malaria vaccine using monkeys as an animal model. Materials and Methods: Blood samples of 274 cynomolgus monkeys (Macaca fascicularis) were collected and identified using microscopy. DNA was extracted from positive blood samples and analyzed using polymerase chain reaction (PCR) to amplify the small subunit ribosomal RNA (SSU rRNA) target gene using consensus primers for Plasmodium species. The PCR-positive samples were then nucleotide-sequenced using commercial sequencing services, analyzed using the BioEdit program, and aligned using Basic Local Alignment Search Tool from the National Center for Biotechnology Information. Phylogenetic trees were constructed using MEGA 11.0 and the neighbor-joining (NJ) method to determine the kinship of Plasmodium. Bootstrapping was performed using 500 replicates to assess the robustness of tree topologies. Results: Thirty-eight of the 274 microscopically positive samples for Plasmodium spp. were also positive using PCR, resulting in a 1640 bp amplicon. Further, analysis using nucleotide sequencing confirmed that these positive samples were Plasmodium inui with more than 99% nucleotide identity compared to GenBank sequences. Phylogenetic tree analysis of the SSU rRNA partial gene showed that all our isolates clustered and were closely related to a P. inui strain isolated from cynomolgus macaques in South China in 2011. Conclusion: P. inui is the predominant malaria parasite in cynomolgus monkeys from Bogor.

Proposal of Helicobacter higonensis sp. nov. isolated from a human clinical specimen, and emended description of Helicobacter valdiviensis Collado, 2014.

We have previously isolated a gram-negative microaerophilic strain, PAGU2000T from a patient presenting with a fever in Kumamoto Prefecture, Japan. The present study aimed to comprehensively analyze the taxonomy of the isolated strain using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that the strain was a member of enterohepatic Helicobacter. The strain PAGU2000T shared a 97.5% 16S rRNA gene nucleotide identity with Helicobacter valdiviensis, and this taxonomic position was confirmed by phylogenetic analysis of the GyrA amino acid sequences. The proposed strain PAGU2000T has a 1.482 Mbp chromosome with a DNA G + C content of 31.3 mol% and encodes 1520 predicted coding sequences. The average nucleotide identity between the strain PAGU2000T and type strain of H. valdiviensis was 70.3%, which was lower than the recommended threshold of 95% for species delineation. The strain PAGU2000T was a motile, non-spore-forming, and spiral-shaped bacterium, exhibiting catalase and oxidase activities but not urease and nitrate reduction. This study demonstrates that the isolate represents a novel species within enterohepatic Helicobacter, for which the name Helicobacter higonensis is proposed (type strain: PAGU2000T = GTC 16811T = LMG 33095T). In this study, we describe the phenotypic and morphological features of this strain and propose an emended description of some biochemical traits of H. valdiviensis.

The First Record of Omsk Hemorrhagic Fever Virus and Tick-Borne Encephalitis Virus of Baltic Lineage from the Kemerovo Region of Russia.

Objectives: Tick-borne encephalitis virus Siberian subtype (TBEV-Sib) and Omsk hemorrhagic fever virus (OHFV) are causative agents of natural focal infections in Western Siberia, Russia. The distribution of TBEV phylogenetic lineages and OHFV in the Kemerovo Region of Western Siberia remains poorly investigated. Methods: The phylogenetic analyses of fragment genome sequences 26 flaviviruses identified in 2019 were performed, and the amino acid variation was determined to reveal to which clusteron they belong. The age of Baltic and Asian lineages of the TBEV-Sib was calculated for Kemerovo District and Region, respectively. Results: Twenty-five isolates were members of three TBEV-Sib phylogenetic lineages: Baltic (48%), Asian (36%), and East Siberian (16%). The Baltic lineage's eastern boundary is commonly thought to be in the Novosibirsk Region, but our data suggest that it may reach further east. Analysis of the Baltic lineage clusteron structure showed that the isolates found are unique (6) or belong to clusteron-founder 3D (1) and derived clusteron 3O (5). Based on the age of 3O clusteron, Baltic lineage could have appeared in the Kemerovo Region by the late 1970s. One of the isolated viruses turned out to be the OHFV of the first subtype and not to belong to any known clusteron. This finding is the first known detection of the virus outside the endemic area of Russia. Given the recent discovery of OHFV in Kazakhstan, it can be assumed that the area of this virus distribution is much wider than previously thought. Conclusions: This report provides insights into the population structure of TBEV and OHFV, which may be helpful for epidemiological investigation and surveillance of the viruses.

First Report of Anthracnose Caused by Colletotrichum spaethianum on Hosta longipes in Korea.

Hosta longipes (Franch. & Sav.) Matsum. (Asparagaceae) is a perennial, herbaceous plant, native to Japan and Korea (Lee et al. 2021). In Korea, the plant is used as an edible vegetable and ornamental (Kang and Ju 2015). During 2021-2022, anthracnose symptoms were observed on leaves of H. longipes with over 70% disease incidence in Wanju-gun (35°38'47''N; 127°31'16''E) and Jangsu-gun (35°35'31''N; 127°30'03''E) in Jeollabuk-do, Korea. The disease initially appeared on old leaves, gradually spreading to young ones. The symptoms were characterized as yellow to white discoloration on the upper leaf surface with black necrotic tissue in the center of the lesion. Three H. longipes samples with anthracnose symptoms were collected. From each, a monoconidial isolate was obtained and then deposited in the Korea Agricultural Culture Collection (accession Nos. KACC 410038, 410391, and 410443). The dried specimens were housed at the herbarium of Jeonbuk National University (JBNU0129, 0137) and Korea University (KUS-F33379). Conidiomata was acervular, 65 to 80 × 56 to 70 µm in diam. Setae were dark brown, 2 to 4-septate, 63 to 161 µm long, being formed on a pale brown cushion. Conidia were hyaline, smooth-walled, aseptate, slightly curved, base truncate, 3.9 to 5.1 × 17 to 23 µm. The appressoria were solitary, olivaceous-brown, ovoid or irregularly shaped. Two-week-old colonies grown on PDA at 25 ℃ were 20-25 mm in diameter, initially white, then turned gray with age, with cottony aerial mycelium. The morphological and cultural characteristics of the fungus were consistent with those of Colletotrichum spaethianum (Allesch.) Damm, P.F. Cannon & Crous (Damm et al. 2012). To confirm morphology-based identification, the nucleotide sequences of the internal transcribed spacer (ITS) rDNA region, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), actin (actA), chitin synthase (CHS1), histone (HIS3) and tubulin (TUB2) genes were determined for KACC410443, as outlined by Cannon et al. (2012) and Damm et al. (2009). The resulting sequences were submitted into GenBank (PP000829 for ITS, PP133094 for GAPDH, PP083418 for actA, PP133091 for CHS1, PP133097 for HIS3, and PP133099 for TUB2) and compared with reference sequences in GenBank using BLASTn search tool. The results showed a 100% match with C. spaethianum (MT611068), C. incanum (MN880260) and C. truncatum (EF016303) for ITS, and 100% with C. spaethianum for GAPDH (MH370513), actA (MH045677), CHS1 (MH370520), HIS3 (MH985161), and TUB (MH456884). Pathogenicity was tested by inoculating conidial suspension (1 ×104 cfu/ml) of three-week-old fungal colonies of the isolate KACC410443 onto leaves of three healthy potted plants. Prior to inoculation, leaves were deliberately wounded by pinpricking with a sterilized needle. Two wounded but non-inoculated plants served as controls. Plants were maintained in a greenhouse at 25 to 30 °C. Inoculated plants developed anthracnose symptoms after eight days, while the control plants remained symptomless. The fungus isolated from the inoculated plants was morphologically identical to that observed initially, fulfilling Koch's postulates. To our knowledge, there is no previous record of C. spaethianum on H. longipes, although C. spaethianum has been reported to infect another species, H. plantaginea (Cheon and Jeon 2016). This is the first report of this fungus on H. longipes in Korea (KSPP 2024) and globally (Farr and Rossman 2024). The anthracnose on this ornamental plant can be considered a new severe threat to planting strategies in gardens.

Identification of B cell subsets based on antigen receptor sequences using deep learning.

B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.

Unravelling the functional and phylogenetic dimensions of novel ecosystem assemblages.

Human activities are causing taxonomic rearrangements across ecosystems that often result in the emergence of novel communities (assemblies with no historical representative). It is commonly assumed that these changes in the taxonomic makeup of ecosystems also inevitably lead to changes in other aspects of biodiversity, namely functional and phylogenetic diversity. However, this assumption is not always valid, as the changes in functional and phylogenetic composition resulting from taxonomic shifts depend on the level of redundancy in the evaluated community. Therefore, we need improved theoretical frameworks to predict when we can expect coordinated or decoupled responses among these three facets of biodiversity. To advance this understanding, we discuss the conceptual and methodological issues that complicate establishing a link between taxonomic rearrangements driven by human activities and the associated functional and phylogenetic changes. Here, we show that is crucial to consider the expected changes in functional and phylogenetic composition as communities are reshaped owing to human drivers of biodiversity loss to forecast the impacts of novel assemblages on ecosystem functions and the services they provide to humanity. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species.

The order Eurotiales is diverse and includes species that impact our daily lives in many ways. In the past, its taxonomy was difficult due to morphological similarities, which made accurate identification of species difficult. This situation improved and stabilised with recent taxonomic and nomenclatural revisions that modernised Aspergillus, Penicillium and Talaromyces. This was mainly due to the availability of curated accepted species lists and the publication of comprehensive DNA sequence reference datasets. This has also led to a sharp increase in the number of new species described each year with the accepted species lists in turn also needing regular updates. The focus of this study was to review the 160 species described between the last list of accepted species published in 2020 until 31 December 2022. To review these species, single-gene phylogenies were constructed and GCPSR (Genealogical Concordance Phylogenetic Species Recognition) was applied. Multi-gene phylogenetic analyses were performed to further determine the relationships of the newly introduced species. As a result, we accepted 133 species (37 Aspergillus, two Paecilomyces, 59 Penicillium, two Rasamsonia, 32 Talaromyces and one Xerochrysium), synonymised 22, classified four as doubtful and created a new combination for Paraxerochrysium coryli, which is classified in Xerochrysium. This brings the number of accepted species to 453 for Aspergillus, 12 for Paecilomyces, 535 for Penicillium, 14 for Rasamsonia, 203 for Talaromyces and four for Xerochrysium. We accept the newly introduced section Tenues (in Talaromyces), and series Hainanici (in Aspergillus sect. Cavernicolarum) and Vascosobrinhoana (in Penicillium sect. Citrina). In addition, we validate the invalidly described species Aspergillus annui and A. saccharicola, and series Annuorum (in Aspergillus sect. Flavi), introduce a new combination for Dichlaena lentisci (type of the genus) and place it in a new section in Aspergillus subgenus Circumdati, provide an updated description for Rasamsonia oblata, and list excluded and recently synonymised species that were previously accepted. This study represents an important update of the accepted species lists in Eurotiales. Taxonomic novelties: New sections: Aspergillus section Dichlaena Visagie, Kocsubé & Houbraken. New series: Aspergillus series Annuorum J.J. Silva, B.T. Iamanaka, Frisvad. New species: Aspergillus annui J.J. Silva, M.H.P. Fungaro, Frisvad, M.H. Taniwaki & B.T. Iamanaka; Aspergillus saccharicola J.J. Silva, Frisvad, M.H.P. Fungaro, M.H. Taniwaki & B.T. Iamanaka. New combinations: Aspergillus lentisci (Durieu & Mont.) Visagie, Malloch, L. Kriegsteiner, Samson & Houbraken; Xerochrysium coryli (Crous & Decock) Visagie & Houbraken. Citation: Visagie CM, Yilmaz N, Kocsubé S, Frisvad JC, Hubka V, Samson RA, Houbraken J (2024). A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Studies in Mycology 107: 1-66. doi: 10.3114/sim.2024.107.01.

Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal.

A novel strain, MA3_2.13T, was isolated from deep-sea sediment of Madeira Archipelago, Portugal, and characterized using a polyphasic approach. This strain produced dark brown soluble pigments, bronwish black substrate mycelia and an aerial mycelium with yellowish white spores, when grown on GYM 50SW agar. The main respiratory quinones were MK-10(H4), MK-10(H6) and MK-10(H8). Diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two glycophospholipids were identified as the main phospholipids. The major cellular fatty acids were iso-C16 : 1, iso-C16 : 0, anteiso-C17 : 1 and anteiso-C17 : 0. Phylogenetic analyses based on 16S rRNA gene showed that strain MA3_2.13T is a member of the genus Streptomyces and was most closely related to Streptomyces triticirhizae NEAU-YY642T (NR_180032.1; 16S rRNA gene similarity 97.9 %), Streptomyces sedi YIM 65188T (NR_044582.1; 16S rRNA gene similarity 97.4 %), Streptomyces mimosae 3MP-10T (NR_170412.1; 16S rRNA gene similarity 97.3 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (NR_133874.1; 16S rRNA gene similarity 97.0 %). Genome pairwise comparisons with closest related type strains retrieved values below the threshold for species delineation suggesting that strain MA3_2.13T represents a new branch within the genus Streptomyces. Based on these results, strain MA3_2.13T (=DSM 115980T=LMG 33094T) is proposed as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces profundus sp. nov. is proposed.

Identification and genomic characterization of feline calicivirus from a leopard cat (Prionailurus bengalensis) in Taiwan.

The leopard cat (Prionailurus bengalensis) is an endangered wildlife that is protected under Taiwan's regulations. The body of a road-killed leopard cat was found to contain sequences of feline calicivirus (FCV), designated W109-1443. Analysis of the complete genomic sequence revealed that it shared approximately 81% similarity with a Chinese strain of FCV found in a domestic cat. Phylogenetic analysis of the VP1 gene indicated that the W109-1443 isolate belonged to genogroup II. Recombination analysis revealed that the W109-1443 isolate may have resulted from recombination between two FCV strains. Given the potential impact of FCV on the health and survival of wild felids, further investigation is necessary to assess its pathogenicity in the leopard cat population.

Occurrence of black queen cell virus in wild bumble bee communities in China.

Wild bumble bees (Hymenoptera: Apidae) play a vital role in agro-ecosystems as important pollinators. However, they are threatened by virus pathogens that are widespread in honey bees. Previous studies have reported that viruses were able to be transmitted across bee genera and caused potential danger to wild bumble bees. China is a global biodiversity hotspot for bumble bees. However, the impact of viruses on the wild bumble bee communities remains elusive. Black queen cell virus (BQCV) is one of the most common honey bee viruses. Here, a total of 72 wild bumble bee samples from 17 geographic regions of China were tested for BQCV. Thirteen positive samples were identified and sequence comparison of partial capsid genes demonstrated a genetic identity of 99.69% to 100%. A phylogenetic tree analysis also showed a close relationship between 13 BQCV isolates and others from a variety of recorded hosts in China. Meanwhile, a distinct evolutionary branch of China isolates was formed when clustering isolates from worldwide bumble bee species. A correlation between BQCV and their geographic locations were observed (P < 0.05). This study not only provides the first evidence of widespread BQCV in wild bumble bee communities in China but also detects a distinct set of genetically identical or closely related BQCV variants that circulate and evolutionarily differ from other countries.

Clonal expansion in normal tissues.

Cancer originates from a single ancestral cell that acquires a driver mutation, which confers a growth or survival advantage, followed by the acquisition of additional driver mutations by descendant cells. Recently, it has become evident that somatic cell mutations accumulate in normal tissues with aging and exposure to environmental factors, such as alcohol, smoking, and UV rays, increases the mutation rate. Clones harboring driver mutations expand with age, leading to tissue remodeling. Lineage analysis of myeloproliferative neoplasms and der(1;16)-positive breast cancer revealed that driver mutations were acquired early in our lives and that the development of cancer takes decades, unveiling the previously unknown early process of cancer development. Evidence that clonal hematopoiesis affects various diseases, including nonneoplastic diseases, highlights the potential role of the identification and functional analysis of mutated clones in unraveling unknown pathologies. In this review, we summarize the recent updates on clonal expansion in normal tissues and the natural history of cancer revealed through lineage analysis of noncancerous and cancerous tissues.

[Site-specific PCR identification of animal species and formula particles of Scorpio].

Scorpio, a commonly used animal medicine in China, is derived from Buthus martensii as recorded in the Chinese Pharmacopoeia. China harbors rich species of Scorpionida and adulterants exist in the raw medicinal material and deep-processed products of Scorpio. The microscopic characteristics of the deep-processed products may be incomplete or lost during processing, which makes the identification difficult. In this study, the maximum likelihood(ML) tree was constructed based on the morphology and cytochrome C oxidase subunit I(COⅠ) to identify the species of Scorpio products. The results showed that the main adulterant of Scorpio was Lychas mucronatus. According to the specific SNP sites in the COⅠ sequence of B. martensii, the stable primers were designed for the identification of the medicinal material and formula granules of Scorpio. The polymerase chain reaction(PCR) at the annealing temperature of 61 ℃ and 30 cycles produced bright specific bands at about 150 bp for both B. martensii and its formula particles and no band for adulterants. The adaptability of the method was investigated, which showed that the bands at about 150 bp were produced for Scorpio medicinal material, lyophilized powder, and formula granules, and commercially available formula granules. The results showed that the established method could be used to identify the adulterants of Scorpio and its formula granules, which could help to improve the quality control system and ensure the safe clinical application of Scorpio formula granules.

An outbreak of COVID-19 after a pilgrimage to Medjugorje due to Delta sub-lineages.

INTRODUCTION: A COVID-19 outbreak occurred at the end of October 2021 among pilgrims returning from Medjugorje (Bosnia and Herzegovina). METHODOLOGY: Whole genome sequencing (WGS) of SARS-CoV-2, epidemiological data, and phylogenetic analysis were used to reconstruct outbreak dynamics. RESULTS: The results suggest that only in one case, associated with the SARS-CoV-2 sub-lineage AY.9.2, it is possible to trace back the place of contagion to Medjugorje, while the other cases were likely to be acquired in the country of origin. CONCLUSIONS: The combined use of phylogenetic data derived from WGS, and epidemiological data allowed us to study epidemic dynamics and to formulate a possible hypothesis on the place of exposure to SARS-CoV-2. The identification of different sub-lineages of the SARS-CoV-2 Delta variant also suggested that different chains of transmission contributed to the outbreak.

Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant.

BACKGROUND: Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported. RESULTS: In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted. CONCLUSIONS: This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.

Rubellicoccus peritrichatus gen. nov., sp. nov., isolated from crustose coralline algae in a coral aquarium.

A Gram-stain-negative, motile, aerobic, non-spore-forming coccus, designated strain CR14T, was isolated from crustose coralline algae. Cells grew at 20-30 °C (optimum, 25 °C), at pH 6-9 (optimum, pH 7.6) and with NaCl concentrations of 0.5-9 % (w/v; optimum, 2-4 %). Global alignment based on 16S rRNA gene sequences indicated strain CR14T is closest to Ruficoccus amylovorans JCM 31066T with an identity of 92 %. The average nucleotide identity and average amino acid identity values between CR14T and R. amylovorans JCM 31066T were 68.4 and 59.9 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CR14T forms an independent branch within the family Cerasicoccaeae, which was consistent with the phylogenomic results. The sole isoprenoid quinone was MK-7. The major fatty acids were C14 : 0, C18 : 1 ω9c, C19 : 0 cyc 9,10 DMA, C16 : 0, and C18 : 2 ω6c. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The genome DNA G+C content was 48.7 mol%. Based on morphological, physiological and chemotaxonomic characteristics, strain CR14T is suggested to represent a novel species in a new genus, for which the name Rubellicoccus peritrichatus gen. nov., sp. nov. is proposed. The type strain is CR14T (=MCCC 1K03845T=KCTC 72139T).