Sequence Analysis Research Articles

Site-Specific N-Glycoprofiling of Immunoglobulin G Subtypes from Donkey Milk.

Donkey milk IgG was probed for the site-specific N-glycosylation pattern through RP-UHPLC-MS/MS. The affinity-purified milk IgG was subjected to SDS-PAGE and proteomic analysis, which revealed the presence of subtypes. Multiple N-glycopeptides arising from the predicted donkey IgG1, IgG2, IgG3, IgG5, IgG6, and IgG7 subtypes' heavy-chain constant region were shown to contain glycans at the highly conserved glycosylation site NST in the CH2 domain. Differences in the peptide backbone with the NST site among subtypes generated after trypsin digestion resulted in the evaluation of the subtype-specific glycan pattern. Glycan sequence analysis indicated predominantly biantennary complex types with core fucosylation at the site NST. Interestingly, an additional site NQT in the CH1 domain of the heavy-chain constant region of IgG5 was found to possess mainly sialylated biantennary complex glycans with NeuAc and NeuGc. Structural diversity of glycans was mainly observed in the predicted donkey IgG1, IgG5, and IgG7, whereas IgG2, IgG3, and IgG6 resulted in the glycopeptides that are of low abundance in the analyzed samples. These findings would pave the way for a better understanding of donkey milk functional properties.

Isolation and phylogenetic analysis of camel contagious ecthyma virus in Morocco

Camel contagious ecthyma is a highly infectious viral skin disease that affects camels and causes economic losses. This study reports the isolation and the phylogenetic analysis of contagious ecthyma virus among camels in Morocco. The disease was detected in four among fifteen camels with severe papules on the lips and nares. Samples of skin crusts were collected and pooled for virus isolation and titration, PCR testing, and histopathological examination. PCR was used to amplify the B2L gene and the resulting product was sequenced and analyzed genetically. The study's findings indicate the presence of characteristic microscopic changes of poxvirus infection in the examined tissues and the virus was isolated on two cells (lambs testis and Vero) and showed distinct growth patterns. The virus grew rapidly on TA cells and delayed growth on Vero cells.The third passage showed cytopathic effects characterized by cell aggregation. Sequence analysis of the B2L gene revealed 100 % similarity to the camel contagious Ecthyma virus isolated from Ethiopia. The camel virus isolates can be classified into two genetic clades according to the B2L gene sequence: the Asian lineage, which includes isolates from Saudi Arabia, Bahrain, and India, and the African lineage, which includes isolates from the Sudan.In conclusion, this is the first instance of the camel contagious ecthyma virus being identified in North Africa in a herd of camels following exposure to stress. Moreover, the progression of the disease was closely monitored from onset to recovery in a setting without the bacterial complication often observed in the field. The virus exhibited opportunistic behavior, exploiting the stress response. Further studies are warranted to evaluate the pathogenicity of the virus in camels and to genetically characterize the circulating virus from different regions. This will be highly beneficial in the development of an appropriate vaccine.

First documentation of whole genome sequence analysis for infectious spleen and kidney necrosis virus (ISKNV) isolated from angel fish (Pterophyllum scalare) in India

The study presents the first report of the ISKNV whole genome sequence isolated from angel fish (Pterophyllum scalare) in India, offering insights into gene composition, function, phylogeny, and potential vaccine development. The complete genome of AK-ISKNV was found to be of 110,460 bp with the GC content of 54.79 %. The complete genome has 122 open reading frames (ORFs) and 48 ORFs were predicted as functional proteins while the rest were hypothetical proteins. Phylogenetic tree constructed based on the major capsid protein and ATPase genes revealed AK-ISKNV in this study belong to the genus Megalocytivirus of the ISKNV-Genotype I. The whole genome exhibits a 99.81 % similarity, and the phylogenetic analysis indicates a close association with Angel Fish Iridovirus (AFIV), specifically identified as MK689685.1, originating from Australia. Further, phylogenetic analysis confirms the ISKNV genotype and its distinction from RSIV. The present study provides the first report of the complete genome sequence and annotation of the ISKNV strain (AK-ISKNV) isolated from India. Four proteins were selected as prospective vaccination candidates based on their high B-cell epitope score and antigenic locations. These proteins include myristylated membrane protein (ORF 105), main capsid protein (ORF 104), and two hypothetical proteins (ORF 11 and ORF 14). In conclusion, this research contributes vital genomic information essential for understanding and mitigating the impact of ISKNV, providing a foundation for targeted disease control measures in aquaculture.

Bacterial Communities Nodulating Lupinus cosentinii Gus. and Their Inputs in the Worldwide Phylogeography of Lupine Endosymbionts

Genetic variability in bacterial populations that nodulate Lupinus cosentinii in Tunisia was investigated. Phylogenetic studies of 40 isolates using recA partial sequences categorized them into three clusters within the Bradyrhizobium genus. Twenty-three strains selected from the three clusters were thoroughly examined through housekeeping genes (recA, glnII and rpoB) multilocus sequence analysis (MLSA). Our results showed that 23 representative strains were distributed in five distinct clusters, with 13 strains belonging to Bradyrhizobium canariense BTA-1T/Bradyrhizobium lupini USDA3051T (10 strains) and Bradyrhizobium hipponense aSej3T (three strains) lineages. Interestingly, eight strains occupied a separate position and could belong to two putative novel Bradyrhizobium species. The nodC phylogeny placed the 23 strains within three symbiovars: genistearum (19 strains), lupini (two strains) and, for the first time, the symbiovar cyanophyllae (two strains). Based on the worldwide phylogeography of rhizobial symbionts nodulating lupine (14 species), our results reported that eight species occurred in more than one continent, and six species were specific for one continent, e.g., Bradyrhizobium rifense, Bradyrhizobium diazoefficiens, Phyllobacterium sp. and Devosia sp. were specific to the African continent, the Bradyrhizobium iriomotense/Bradyrhizobium stylosanthis group to America, and Bradyrhizobium valentinum to the European continent.

Isolation of Bacillus Velezensis from Leepuram Sea Sediment and Its Bioactive Compound and Antimicrobial Activity

Research into marine bacteria in India for their potential active chemicals is essential for the creation of medications derived from marine sources. The objective of this research was to collect Bacillus velezensis from Leepuram Sea Sediment, test their antibacterial efficacy with the agar diffusion method, and find secondary metabolites by GC-MS spectroscopy.Traditional microbiological methods and phylogenetic analysis of 16S rRNA sequences were used to successfully identify Bacillus velezensis from sediment samples obtained in the Leepuram Sea, Kanyakumari. Using the agar well diffusion method, we tested the isolated metabolites for their antibacterial activity against Gram-positive and Gram-negative bacteria. The results showed that the extract had a strong antibacterial effect, inhibiting the growth of harmful bacteria with zones of inhibition as large as 19 mm for E. coli and Pseudomonas.Bacillus velezensis produces secondary metabolites with pharmacological potential, according to this study. These metabolites may have useful uses in biocontrol, agriculture, and medicine. The implications of these results for human health and the creation of new antimicrobial drugs are likely to grow substantially when more worldwide research is carried out.

Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays

Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed.Key points• The applied methodology was successful to obtain biomass suitable to perform BMP assays.• The microbial community was resilient to external biomass addition.• Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.Graphical

Metagenomics analysis of bacterial community structure from wood- and soil-feeding termites: metabolic pathways and functional structures toward the degradation of lignocellulose and recalcitrant compounds.

Some essential information on gut bacterial profiles and their unique contributions to food digestion in wood-feeding termites (WFT) and soil-feeding termites (SFT) is still inadequate. The feeding type of termites is hypothesized to influence their gut bacterial composition and its functionality in degrading lignocellulose or other organic chemicals. This could potentially provide alternative approaches for the degradation of some recalcitrant environmental chemicals. Therefore, metagenomic analysis can be employed to examine the composition and functional profiles of gut bacterial symbionts in WFT and SFT. Based on the metagenomic analysis of the 16S rRNA gene sequences of gut bacterial symbionts in the WFT, Microcerotermes sp., and the SFT, Pericapritermes nitobei, the findings revealed a total of 26 major bacterial phyla, with 18 phyla commonly represented in both termites, albeit in varying abundances. Spirochaetes dominated the bacterial symbionts in Microcerotermes sp. at 55%, followed by Fibrobacters, while Firmicutes dominated the gut bacteria symbionts in P. nitobei at 95%, with Actinobacteria coming in second at 2%. Furthermore, the Shannon and phylogenetic tree diversity indices, as well as the observed operational taxonomic units and Chao 1 richness indices, were all found to be higher in the WFT than in the SFT deduced from the alpha diversity analysis. Based on the principal coordinate analysis, exhibited a significant distance dissimilarity between the gut bacterial symbionts. The results showed that the gut bacterial composition differed significantly between the WFT and SFT. Furthermore, Tax4Fun analysis evaluated bacterial functions, revealing the predominance of carbohydrate metabolism, followed by amino acid metabolism and energy metabolism in both Microcerotermes sp. and P. nitobei termites. The results implicated that bacterial symbionts inhabiting the guts of both termites were actively involved in the degradation of lignocellulose and other recalcitrant compounds.

Sulfonamide-Based Inhibition of the β-Carbonic Anhydrase from A. baumannii, a Multidrug-Resistant Bacterium.

Acinetobacter baumannii is a Gram-negative opportunistic pathogen responsible for severe hospital-associated infections. Owing to its ability to develop resistance to a wide range of antibiotics, novel therapeutic strategies are urgently needed. One promising approach is to target bacterial carbonic anhydrases (CAs; EC 4.2.1.1), which are enzymes critical for various metabolic processes. The genome of A. baumannii encodes a β-CA (βAbauCA), which is essential for producing bicarbonate ions required in the early stages of uridine triphosphate (UTP) synthesis, a precursor for the synthesis of peptidoglycans, which are vital components of the bacterial cell wall. This study aimed to inhibit βAbauCA in vitro, with the potential to impair the vitality of the pathogen in vivo. We conducted sequence and structural analyses of βAbauCA to explore its differences from those of human CAs. Additionally, kinetic and inhibition studies were performed to investigate the catalytic efficiency of βAbauCAβ and its interactions with sulfonamides and their bioisosteres, classical CA inhibitors. Our results showed that βAbauCA has a turnover rate higher than that of hCA I but lower than that of hCA II and displays distinct inhibition profiles compared to human α-CAs. Based on the obtained data, there are notable differences between the inhibition profiles of the human isoforms CA I and CA II and bacterial βAbauCA. This could open the door to designing inhibitors that selectively target bacterial β-CAs without affecting human α-CAs, as well as offer a novel strategy to weaken A. baumannii and other multidrug-resistant pathogens.

Natural Co-Infections of Aeromonas veronii and Yellow Catfish Calicivirus (YcCV) in Ascites Disease Outbreaks in Cultured Yellow Catfish: An Emerging Fish Disease in China.

Yellow catfish is one of the most important aquaculture species in China, with an annual output of 565,000 tons. Between May and July 2022, the farmed yellow catfish experienced an unusually high mortality rate in an aquaculture farm next to Futou Lake in Hubei, China. Diseased fish exhibited symptoms including ascites, skin ulcers, and bleeding in the head, oral cavity, and lower jaw base. Polymerase chain reaction (PCR) and sequence analyses confirmed the co-infection of Yellow Catfish Calicivirus (YcCV) and Aeromonas veronii in the diseased fish. Transmission electron microscopy exposed abundant virus particles within kidney and spleen cells, characterized by their spherical shape and approximate diameter of 35 nm. Historically, the ascites disease in yellow catfish has been predominantly attributed to bacterial infections over the past two decades. This study represents the first documentation of a correlation between the ascites disease of yellow catfish and the natural co-infection of YcCV and Aeromonas veronii. The findings suggest a possible synergistic interaction between YcCV and bacterial pathogens, potentially aggravating disease severity in yellow catfish aquaculture.

Genome-wide identification, transcript profiling and functional analyses of PCP gene family in Wucai (Brassica campestris)

Pollen coat proteins (PCPs) are cysteine-rich small-molecule proteins, which exhibit high levels of polymorphism and are expressed in gametocytes. Previous investigations have revealed that PCP genes are involved in pollen wall synthesis, pollen-stigma recognition, and pollen development and germination. However, gene expression and function of PCP family in pollen development is not well understood in Wucai (Brassica campestris L.). In this study, genome-wide identification and expression analysis of the BcPCP gene family members were conducted, including their physical and chemical properties, chromosome localization, phylogenetic relationships, gene structure, and tertiary structure. A total of 20 BcPCP genes were identified and classified into three subfamilies showing high homology to Arabidopsis thaliana. Expression pattern analysis indicated that the BcPCP gene family exhibits higher expression levels in reproductive organs, suggesting their potential involvement in the reproductive development. Notably, BraA02g002400.3 C, potentially associated with male sterility, was identified through multiple transcriptomic and proteomic datasets. Subsequently, sequence analysis revealed its homology with the Arabidopsis GRP20 gene, and thus it was named BcGRP20. Functional analysis of this gene showed that overexpression of BcGRP20 gene in the Arabidopsis grp20 mutant could restore anther fertility. Overall, our findings indicate that BcGRP20 plays a critical role in pollen development and may be the causative gene for male sterility in Wucai. This study provides candidate genes for further functional identification of BcPCP genes in Wucai, which are crucial for anther development.

The Expression and Sequence Analysis of MdMATE52 in Apple Roots During Activation of Defense Against Pythium ultimum Infection

To understand the molecular regulation of host defense responses in the pathosystem between apple roots and a necrotrophic oomycete pathogen Pythium ultimum, a series of transcriptome analyses have revealed a multi-phase and multi-layer defense tactic in apple root tissues. Among the most notable transcriptome changes during defense activation in apple roots, upregulation of genes involved in phenylpropanoid biosynthesis, transport of secondary metabolites, and lignin formation appeared to be the key defense themes which may crucially impact the outcome of plant–pathogen interactions. From our transcriptome datasets, the MdMATE52 gene, which encodes a MATE transporter, was shown to be differentially expressed between a resistant and a susceptible apple rootstock genotype in response to P. ultimum infection. The cis elements at promoter regions and sequence variations within coding regions of MdMATE52 were compared among several resistant and susceptible apple rootstock genotypes as well as various Malus species. The stronger upregulated expression patterns of MdMATE52 appeared to be correlated with the observed resistance traits among various genotypes. Our results suggested that minimal but clearly identifiable sequence variations may contribute to the genotype-specific expression and function of MdMATE52. The findings from this study should facilitate future experiments such as site-specific mutation and Crispr-based genome editing to define the regulation mechanisms of MdMATE52 and function during defense activation in apple roots.

A distinct Borrelia clade within the relapsing fever group from cat-infesting Haemaphysalis semermis Neumann 1901 (Acari: Ixodidae).

An undescribed relapsing fever group Borrelia species was detected in a male Haemaphysalis semermis tick infesting a rural cat in an indigenous population in Pahang National Park, Peninsular Malaysia. The 16S rRNA gene sequence revealed close similarity of this variant to several undescribed Borrelia species and Borrelia theileri, with genetic distances ranging from 0.58 to 0.72%. Furthermore, the flaB, gyrB, and the concatenated 16S rRNA + flaB + gyrB sequence analyses demonstrated that this variant is distinctly separated from multiple undescribed Borrelia species, Borrelia miyamotoi, and B. theileri, with genetic distances ranging from 3.41 to 7.00%. This study not only reports the first Borrelia found in H. semermis but also suggests that it forms a distinct clade within the relapsing fever group in Peninsular Malaysia.

Occurrence and assemblage distribution of Giardia Duodenalis in symptomatic and asymptomatic patients in southeastern Iran (2019–2022)

BackgroundThe ubiquitous protozoan parasite Giardia duodenalis is a major contributor to the global burden of diarrhoea, particularly in young children living in poor-resource regions. Although rarely mortal, giardiasis is associated with growth retardation and cognitive impairment in early childhood. Here we investigate the epidemiology of human giardiasis in Iranshahr (south-eastern Iran), a region where this information was previously lacking.MethodsStool samples were collected from 17,455 outpatients and inpatients attended at three major hospital settings during April 2020 and March 2022. Microscopy was used as a screening method for the presence of Giardia cysts, and the identification of G. duodenalis assemblages was carried out using PCR and Sanger sequencing.ResultsThe overall prevalence of giardiasis was 1.87 (326/17,455; 95% CI: 1.7–2.1). Being female was positively associated with higher odds of giardiasis (p = 0.014). Individuals without diarrhoea were less likely to have giardiasis (p = 0.022). Individuals attending the Iran Hospital were more likely to harbour G. duodenalis infections compared to those attending at the Khatam Hospital and the Clinical Reference Laboratory (p = 0.001). Our sequence analyses revealed the presence of assemblages A (56.5%, 13/23), B (39.1%, 9/23), and A + B (4.4%, 1/23). No association was observed between the occurrence of a given assemblage and the occurrence of diarhroea.ConclusionsGiardia infections were found at relatively low prevalence rates in both symptomatic and asymptomatic individuals seeking medical attention. Being female, having diarrhoea, and being sampled during 2020–21 were predictors of giardiasis. Although limited, our molecular data indicate that some Giardia infections may be zoonotic in nature. These data should be corroborated and expanded in future epidemiological studies targeting simultaneously human, animal, and environmental (water) samples to improve our understanding of the epidemiology of giardiasis in Iran.

Chloroplast Genome and Description of Borodinellopsis insignis sp. nov. (Chlamydomonadales, Chlorophyta), a Rare Aerial Alga from China.

The genus Borodinellopsis is extremely rare and is the subject of limited research and reports. It currently comprises only two species, Borodinellopsis texensis and Borodinellopsis oleifera, which differ from other globose algae due to their unique centrally radiating chloroplasts. In this study, we describe a new specimen in detail based on morphological data and phylogenetic analysis and identify it as B. insignis. B. insignis and B. texensis exhibit a high degree of similarity, likely due to their shared characteristics of centrally radiating chloroplasts and flagella that are significantly longer than the cell body. A phylogenetic tree constructed based on the 18S rDNA sequence indicates that B. insignis and B. texensis form a branch that is distinct from other genera, such as Tetracystis, Spongiococcum, and Chlorococcum. Phylogenetic analysis of the ITS sequence, the rbcL gene, and the tufA gene reveals that B. insignis is significantly different from B. texensis, in that it has oil droplets, smaller vegetative cells and zoospores, and distinct habitats. It is also different from B.oleifera as it has smaller vegetative cells and zoospores, turns red after cultivation, has longer flagella, and resides in different habitats. The chloroplast genomes of B. texensis and B. insignis further show significant differences, with the phylogenetic tree constructed based on the analysis of 49 protein-coding genes forming two separate branches. The collinearity of the chloroplast genomes in B. texensis and B. insignis is poor, with 15 out of the 31 homologous modules displaying inversions and complex rearrangements. Given these differences, we classify this alga as a new species and named it Borodinellopsis insignis sp. nov.

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.

Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis, multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS embeddings accurately represented pairwise genetic distances including the intermediate placement of recombinant SARS-CoV-2 lineages between parental lineages. Clusters from t-SNE embeddings accurately recapitulated known phylogenetic clades, H3N2 reassortment groups, and SARS-CoV-2 recombinant lineages. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.

Ultra-Selective and Sensitive Fluorescent Chemosensor Based on Phage Display-Derived Peptide with an N-Terminal Cu(II)-Binding Motif.

Copper, along with gold, was among the first metals that humans employed. Thus, the copper pollution of the world's water resources is escalating, posing a significant threat to human health and aquatic ecosystems. It is crucial to develop detection technology that is both low-cost and feasible, as well as ultra-selective and sensitive. This study explored the use of the NH2-Xxx-His motif-derived peptide from phage display technology for ultra-selective Cu2+ detection. Various Cu-binding M13 phage clones were isolated, and their affinity and cross-reactivity for different metal ions were determined. A detailed analysis of the amino acid sequence of the unique Cu-binding peptides was employed. For the development of an optical chemosensor, a peptide with an NH2-Xxx-His motif was selected. The dansyl group was incorporated during solid-phase peptide synthesis, and fluorescence detection assays were employed. The efficacy of the Cu2+-binding peptide was verified through spectroscopic measurements. In summary, we developed a highly selective and sensitive fluorescent chemosensor for Cu2+ detection based on a peptide sequence from a phage display library that carries the N-terminal Xxx-His motif.

Diplomonorchis fallax n. sp. (Digenea: Monorchiidae) from the northern Gulf of Mexico with evaluation of sympatric congeners

Diplomonorchis micropogoni Nahhas & Cable, 1964 was considered a junior subjective synonym of Diplomonorchis leiostomi Hopkins, 1941 in 1969. Diplomonorchis leiostomi has since been widely reported from the coastal Western Atlantic between Delaware Bay and southern Brazil. Until now, taxonomically verifiable DNA sequence data for D. leiostomi has been available from an individual worm collected from the northern Gulf of Mexico. We generated a partial sequence of the 28S rRNA gene from D. leiostomi from the spot croaker, Leiostomus xanthurus Lacepède (type-host) from Beaufort, North Carolina, USA (type-locality) that differed at 31 of 1,246 bases from the available 28S sequence. This prompted a reevaluation of Diplomonorchis spp. identities from the northern Gulf of Mexico. We found D. leiostomi and D. micropogoni distinguishable by testes shape and size, and to a lesser degree by relative caecal length. Museum specimens of D. leiostomi, identified from the Gulf of Mexico represent a species complex containing D. leiostomi, D. cf. micropogoni and, a new species of Diplomonorchis. The sequences previously identified as D. leiostomi in GenBank (AY222137 & AY222252) are herein identified as D. cf. micropogoni. The new species is described from newly collected material herein. Phylogenetic analysis of 28S rRNA sequences from the species complex plus 46 species from the Monorchioidea Odhner, 1911 indicated all three Diplomonorchis spp. are closely related and form a clade with some species of Lasiotocus Looss, 1907. With the addition of the new species, and acceptance of D. micropogoni, there are currently 14 valid species in Diplomonorchis.

Dengue virus genomic surveillance in the applying Wolbachia to eliminate dengue trial reveals genotypic efficacy and disruption of focal transmission

Release of Aedes aegypti mosquitoes infected with Wolbachia pipientis (wMel strain) is a biocontrol approach against Ae. aegypti-transmitted arboviruses. The Applying Wolbachia to Eliminate Dengue (AWED) cluster-randomised trial was conducted in Yogyakarta, Indonesia in 2018–2020 and provided pivotal evidence for the efficacy of wMel-Ae. aegypti mosquito population replacement in significantly reducing the incidence of virologically-confirmed dengue (VCD) across all four dengue virus (DENV) serotypes. Here, we sequenced the DENV genomes from 318 dengue cases detected in the AWED trial, with the aim of characterising DENV genetic diversity, measuring genotype-specific intervention effects, and inferring DENV transmission dynamics in wMel-treated and untreated areas of Yogyakarta. Phylogenomic analysis of all DENV sequences revealed the co-circulation of five endemic DENV genotypes: DENV-1 genotype I (12.5%) and IV (4.7%), DENV-2 Cosmopolitan (47%), DENV-3 genotype I (8.5%), and DENV-4 genotype II (25.7%), and one recently imported genotype, DENV-4 genotype I (1.6%). The diversity of genotypes detected among AWED trial participants enabled estimation of the genotype-specific protective efficacies of wMel, which were similar (± 10%) to the point estimates of the respective serotype-specific efficacies reported previously. This indicates that wMel afforded protection to all of the six genotypes detected in Yogyakarta. We show that within this substantial overall viral diversity, there was a strong spatial and temporal structure to the DENV genomic relationships, consistent with highly focal DENV transmission around the home in wMel-untreated areas and a near-total disruption of transmission by wMel. These findings can inform long-term monitoring of DENV transmission dynamics in Wolbachia-treated areas including Yogyakarta.

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters.

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC's data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others') through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

A large-scale screening identifies receptor-like kinases with common features in kinase domains that are potentially related to disease resistance in planta.

The plant genome encodes a plethora of proteins with structural similarity to animal receptor protein kinases, collectively known as receptor-like protein kinases (RLKs), which predominantly localize to the plasma membrane where they activate their kinase domains to convey extracellular signals to the interior of the cell, playing crucial roles in various signaling pathways. Despite the large number of members within the RLK family, to date, only a few have been identified as pattern-recognition receptors (PRRs), leaving many potential RLKs that could play roles in plant immunity undiscovered. In this study, a recombinant strategy was initially employed to screen the kinase domains of 133 RLKs in the Arabidopsis genome to determine their involvement in the pathogen-triggered immunity (PTI) pathway. Subsequently, 6 potential immune-related recombinant RLKs (rRLKs) were selected for the creation of transgenic materials and underwent functional characterization analysis. Finally, a sequence analysis was conducted on the kinase domains of these 133 RLKs as well as the known immune RLK receptor kinase domains from other species. It was found that 24 rRLKs activated the PTI response in Arabidopsis fls2 mutant protoplasts following flg22 treatment. Consistently, when 6 of these rRLKs were individually expressed in fls2 background, they exhibited diverse PTI signal transduction capabilities via different pathways while all retained membrane localization. Intriguingly, sequence analysis revealed multiple conserved amino acid sites within kinase domains of these experimentally identified immune-related RLKs in Arabidopsis. Importantly, these patterns are also preserved in RLKs involved in PTI in other species. This study, on one hand, identifies common features that theoretically can enhance our understanding of immune-related RLKs and facilitate the discovery of novel immune-related RLKs in the future. On the other hand, it provides experimental evidence for the use of recombinant technique to develop diverse rRLKs for molecular breeding, thereby conferring high resistance to plants without compromising their normal growth and development.