Phylogenetic Clustering Research Articles

Identifying novel sources of resistance to wheat stem sawfly in five wild wheat species.

The wheat stem sawfly (WSS, Cephus cinctus) is a major pest of wheat (Triticum aestivum) and can cause significant yield losses. WSS damage results from stem boring and/or cutting, leading to the lodging of wheat plants. Although solid-stem wheat genotypes can effectively reduce larval survival, they may have lower yields than hollow-stem genotypes and show inconsistent solidness expression. Because of limited resistance sources to WSS, evaluating diverse wheat germplasm for novel resistance genes is crucial. We evaluated 91 accessions across five wild wheat species (Triticum monococcum, T. urartu, T. turgidum, T. timopheevii, and Aegilops tauschii) and common wheat cultivars (T. aestivum) for antixenosis (host selection) and antibiosis (host suitability) to WSS. Host selection was measured as the number of eggs after adult oviposition, and host suitability was determined by examining the presence or absence of larval infestation within the stem. The plants were grown in the greenhouse and brought to the field for WSS infestation. In addition, a phylogenetic analysis was performed to determine the relationship between the WSS traits and phylogenetic clustering. Overall, Ae. tauschii, T. turgidum and T. urartu had lower egg counts and larval infestation than T. monococcum, and T. timopheevii. T. monococcum, T. timopheevii, T. turgidum, and T. urartu had lower larval weights compared with T. aestivum. This study shows that wild relatives of wheat could be a valuable source of alleles for enhancing resistance to WSS and identifies specific germplasm resources that may be useful for breeding. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Geographical and temporal distribution of multidrug-resistant Salmonella Infantis in Europe and the Americas.

Recently emerged S. Infantis strains carrying resistance to several commonly used antimicrobials have been reported from different parts of the globe, causing human cases of salmonellosis and with occurrence reported predominantly in broiler chickens. Here, we performed phylogenetic and genetic clustering analyses to describe the population structure of 417 S. Infantis originating from multiple European countries and the Americas collected between 1985 and 2019. Of these, 171 were collected from 56 distinct premises located in England and Wales (E/W) between 2009 and 2019, including isolates linked to incursions of multidrug-resistant (MDR) strains from Europe associated with imported poultry meat. The analysis facilitated the comparison of isolates from different E/W sources with isolates originating from other countries. There was a high degree of congruency between the outputs of different types of population structure analyses revealing that the E/W and central European (Germany, Hungary, and Poland) isolates formed several disparate groups, which were distinct from the cluster relating to the United States (USA) and Ecuador/Peru, but that isolates from Brazil were closely related to the E/W and the central European isolates. Nearly half of the analysed strains/genomes (194/417) harboured the IncFIB(pN55391) replicon typical of the "parasitic" pESI-like megaplasmid found in diverse strains of S. Infantis. The isolates that contained the IncFIB(pN55391) replicon clustered together, despite originating from different parts of the globe. This outcome was corroborated by the time-measured phylogeny, which indicated that the initial acquisition of IncFIB(pN55391) likely occurred in Europe in the late 1980s, with a single introduction of IncFIB(pN55391)-carrying S. Infantis to the Americas several years later. Most of the antimicrobial resistance (AMR) genes were identified in isolates that harboured one or more different plasmids, but based on the short-read assemblies, only a minority of the resistance genes found in these isolates were identified as being associated with the detected plasmids, whereas the hybrid assemblies comprising the short and long reads demonstrated that the majority of the identified AMR genes were associated with IncFIB(pN55391) and other detected plasmid replicon types. This finding underlies the importance of applying appropriate methodologies to investigate associations of AMR genes with bacterial plasmids.

Bacterial cytochrome P450s: a bioinformatics odyssey of substrate discovery.

Bacterial P450 cytochromes (BacCYPs) are versatile heme-containing proteins responsible for oxidation reactions on a wide range of substrates, contributing to the production of valuable natural products with limitless biotechnological potential. While the sequencing of microbial genomes has provided a wealth of BacCYP sequences, functional characterization lags behind, hindering our understanding of their roles. This study employs a comprehensive approach to predict BacCYP substrate specificity, bridging the gap between sequence and function. We employed an integrated approach combining sequence and functional data analysis, genomic context exploration, 3D structural modeling with molecular docking, and phylogenetic clustering. The research begins with an in-depth analysis of BacCYP sequence diversity and structural characteristics, revealing conserved motifs and recurrent residues in the active site. Phylogenetic analysis identifies distinct groups within the BacCYP family based on sequence similarity. However, our study reveals that sequence alone does not consistently predict substrate specificity, necessitating additional perspectives. The study delves into the genetic context of BacCYPs, utilizing neighboring gene information to infer potential substrates, a method proven very effective in many cases. Molecular docking is employed to assess BacCYP-substrate interactions, confirming potential substrates and providing insights into selectivity. Finally, a comprehensive strategy is proposed for predicting BacCYP substrates, involving all the evaluated approaches. The effectiveness of this strategy is demonstrated with two case studies, highlighting its potential for substrate discovery.

Constructing a database of alien plants in the Himalaya to test patterns structuring diversity.

Differences in the number of alien plant species in different locations may reflect climatic and other controls that similarly affect native species and/or propagule pressure accompanied with delayed spread from the point of introduction. We set out to examine these alternatives for Himalayan plants, in a phylogenetic framework. We build a database of alien plant distributions for the Himalaya. Focusing on the well-documented regions of Jammu & Kashmir (west) and Bhutan (east) we compare alien and native species for (1) richness patterns, (2) degree of phylogenetic clustering, (3) the extent to which species-poor regions are subsets of species-rich regions and (4) continental and climatic affinities/source. We document 1470 alien species (at least 600 naturalised), which comprise ~14% of the vascular plants known from the Himalaya. Alien plant species with tropical affinities decline in richness with elevation and species at high elevations form a subset of those at lower elevations, supporting location of introduction as an important driver of alien plant richness patterns. Separately, elevations which are especially rich in native plant species are also rich in alien plant species, suggesting an important role for climate (high productivity) in determining both native and alien richness. We find no support for the proposition that variance in human disturbance or numbers of native species correlate with alien distributions. Results imply an ongoing expansion of alien species from low elevation sources, some of which are highly invasive.

Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses.

Understanding phylogenetic relationships among species is essential for many biological studies, which call for an accurate phylogenetic tree to understand major evolutionary transitions. The phylogenetic analyses present a major challenge in estimation accuracy and computational efficiency, especially recently facing a wave of severe emerging infectious disease outbreaks. Here, we introduced a novel, efficient framework called Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) for new sample placement for viruses. In this study, a brand-new recoding method called Frequency Vector Recoding was implemented to approximate the phylogenetic distance, and the Phylogenetic Simulated Annealing Search algorithm was developed to match the recoded distance matrix with the phylogenetic tree. Meanwhile, the indel (insertion/deletion) was heuristically introduced to foreign sequence recognition for the first time. Here, we compared the Bd-RPC with the recent placement software (PAGAN2, EPA-ng, TreeBeST) and evaluated it in Alphacoronavirus, Alphaherpesvirinae, and Betacoronavirus by using Split and Robinson-Foulds distances. The comparisons showed that Bd-RPC maintained the highest precision with great efficiency, demonstrating good performance in new sample placement on all three virus genera. Finally, a user-friendly website (http://www.bd-rpc.xyz) is available for users to classify new samples instantly and facilitate exploration of the phylogenetic research in viruses, and the Bd-RPC is available on GitHub (http://github.com/Bin-Ma/bd-rpc).

Decoding the Genomic Landscape of Pomegranate: A Genome-Wide Analysis of Transposable Elements and Their Structural Proximity to Functional Genes

Transposable elements (TEs) significantly drive dynamic changes that characterize genome evolution. However, understanding the variability associated with TE insertions among different cultivars remains challenging. The pomegranate (Punica granatum L.) has yet to be extensively studied regarding the roles of TEs in the diversification of cultivars. Herein, we explored the genome distribution of TEs and its potential functional implications among four pomegranate cultivars, ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’ and ‘Tunisia’, whose genome sequences are available. A total of 8404 full-length TEs were isolated. The content of TEs varied among the cultivars, ranging from 41.67% of ‘Taishanhong’ to 52.45% of ‘Bhagwa’. In all cultivars, the Gypsy superfamily of retrotransposons accounted for a larger genome proportion than the Copia superfamily. Seventy-three full-length TEs were found at the same genomic loci in all four cultivars. By contrast, 947, 297, 311, and 874 TEs were found exclusively in ‘Bhagwa’, ‘Dabenzi’, ‘Taishanhong’, and ‘Tunisia’ cultivars, respectively. Phylogenetic clustering based on the presence of TE insertions in specific loci reflected the geographic origins of the cultivars. The insertion time profiles of LTR-REs were studied in the four cultivars. Shared elements across the four cultivars exhibited, on average, a more ancient insertion date than those exclusive to three, two, or one cultivars. The majority of TEs were located within 1000 bp from the nearest gene. This localization was observed for 57% of DNA TEs and 55% of long-terminal repeat retrotransposons (LTR-RE). More than 10% of TEs resulted inserted within genes. Concerning DNA TEs, 3.91% of insertions occurred in introns, while 2.42% occurred in exons. As to LTR-REs, 4% of insertions occurred in exons and 1.98% in introns. Functional analysis of the genes lying close to TEs was performed to infer if differences in TE insertion can affect the fruit quality. Two TE insertions were found close to two genes encoding 4-coumarate--CoA ligase, an enzyme involved in the phenylpropanoid pathway. Moreover, a TIR/Mariner element was found within the exon of a gene encoding anthocyanidin reductase in the ‘Tunisia’ genotype, crucial in the biosynthesis of flavan-3-ols and proanthocyanidins, strictly correlated with the nutraceutical properties of pomegranate. Although functional and metabolomic studies are essential to elucidate the consequences of TE insertions, these results contribute to advancing our comprehension of the role of TEs in pomegranate genomics, providing insights for crop breeding.

Prison as a driver of recent transmissions of multidrug-resistant tuberculosis in Callao, Peru: a cross-sectional study

We sought to identify resistance patterns and key drivers of recent multidrug-resistant tuberculosis (MDR-TB) transmission in a TB-prevalent area in Peru. Cross-sectional study including MDR Mycobacterium tuberculosis complex (Mtbc) strains identified in Callao-Peru between April 2017 and February 2019. Mtbc DNA was extracted for whole genome sequencing which was used for phylogenetic inference, clustering, and resistance mutation analyses. Clusters indicative of recent transmission were defined based on a strain-to-strain distance of ≤5 (D5) single nucleotide polymorphisms (SNPs). Epidemiologic factors linked to MDR-TB clustering were analyzed using Poisson regression. 171 unique MDR-Mtbc strains were included; 22 (13%) had additional fluoroquinolone resistance and were classified as pre-XDR. Six strains (3.5%) harboured bedaquiline (BDQ) resistance mutations and were classified as MDR+BDQ. 158 (92%) Mtbc strains belonged to lineage 4 and 13 (8%) to lineage 2. Using a cluster threshold of ≤5 SNPs, 98 (57%) strains were grouped in one of the 17 D5 clusters indicative of recent transmission, ranging in size from 2 to the largest cluster formed by 53 4.3.3 strains (group_1). Lineage 4.3.3 strains showed the overall highest cluster rate (43%). In multivariate analyses, current or previous imprisonment was independently associated with being part of any MDR-TB transmission clusters (adjusted prevalence ratio [aPR], 1.45; 95% CI, 1.09-1.92). Pre-XDR-TB emerged in more than 10% of the MDR-TB strains investigated. Transmission of 4.3.3 Mtbc strains especially of the dominant group_1 clone is a major driver of the MDR-TB epidemic in Callao. Current or previous imprisonment was linked to recent MDR-TB transmissions, indicating an important role of prisons in driving the MDR-TB epidemic. This work was supported in part by the ERANet-LAC Network of the European Union, Latin America and the Caribbean Countries on Joint Innovation and Research Activities, and FONDECYT. Additional support was received from Leibniz Science Campus Evolutionary Medicine of the Lung, the Deutsche Forschungsgemeinschaft (German Research Foundation, under Germany's Excellence Strategy-EXC 2167 Precision Medicine in Inflammation), and the Research Training Group 2501 TransEvo.

DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China.

Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.

Molecular Characteristics of Staphylococcus aureus Isolates form Food-Poisoning Outbreaks (2011-2022) in Sichuan, China.

Staphylococcal food poisoning (SFP) is one of the most common foodborne diseases in the world. This study aimed to investigate the molecular epidemiological characteristics of Staphylococcus aureus isolated from SFP. A total of 103 S. aureus isolates were obtained during 2011-2022 in Sichuan, southwest China. All isolates were tested for the genomic characteristics and phylogenetic analysis by performing whole-genome sequencing. Multilocus sequence typing analysis showed 17 multilocus sequence types (STs), ST7 (23.30%), ST5 (22.33%), and ST6 (16.50%) being the most common. A total of 45 virulence genes were detected, 22 of which were staphylococcal enterotoxin (SE) genes. Among the identified SE genes, selX exhibited the highest prevalence (86.4%). All isolates carried at least one SE gene. The results of the antimicrobial resistance (AMR) gene detection revealed 41 AMR genes of 12 classes. β-lactam resistance genes (blal, blaR1, blaZ) and tetracycline resistance gene (tet(38)) exhibited a higher prevalence rate. Core genome single nucleotide polymorphism showed phylogenetic clustering of the isolates with the same region, year, and ST. The results indicated that the SFP isolates in southwest of China harbored multiple toxin and resistance genes, with a high prevalence of new SEs. Therefore, it is important to monitor the antimicrobial susceptibility and SE of S. aureus to reduce the potential risks to public health.

The Calcium-Dependent Protein Kinase TaCDPK7 Positively Regulates Wheat Resistance to Puccinia striiformis f. sp. tritici.

Ca2+ plays a crucial role as a secondary messenger in plant development and response to abiotic/biotic stressors. Calcium-dependent protein kinases (CDPKs/CPKs) are essential Ca2+ sensors that can convert Ca2+ signals into downstream phosphorylation signals. However, there is limited research on the function of CDPKs in the context of wheat-Puccinia striiformis f. sp. tritici (Pst) interaction. In this study, we aimed to address this gap by identifying putative CDPK genes from the wheat reference genome and organizing them into four phylogenetic clusters (I-IV). To investigate the expression patterns of the TaCDPK family during the wheat-Pst interaction, we analyzed time series RNA-seq data and further validated the results through qRT-PCR assays. Among the TaCDPK genes, TaCDPK7 exhibited a significant induction during the wheat-Pst interaction, suggesting that it has a potential role in wheat resistance to Pst. To gain further insights into the function of TaCDPK7, we employed virus-induced gene silencing (VIGS) to knock down its expression which resulted in impaired wheat resistance to Pst, accompanied by decreased accumulation of hydrogen peroxide (H2O2), increased fungal biomass ratio, reduced expression of defense-related genes, and enhanced pathogen hyphal growth. These findings collectively suggest that TaCDPK7 plays an important role in wheat resistance to Pst. In summary, this study expands our understanding of wheat CDPKs and provides novel insights into their involvement in the wheat-Pst interaction.

AutoPhy: Automated phylogenetic identification of novel protein subfamilies.

Phylogenetic analysis of protein sequences provides a powerful means of identifying novel protein functions and subfamilies, and for identifying and resolving annotation errors. However, automation of functional clustering based on phylogenetic trees has been challenging and most of it is done manually. Clustering phylogenetic trees usually requires the delineation of tree-based thresholds (e.g., distances), leading to an ad hoc problem. We propose a new phylogenetic clustering approach that identifies clusters without using ad hoc distances or other pre-defined values. Our workflow combines uniform manifold approximation and projection (UMAP) with Gaussian mixture models as a k-means like procedure to automatically group sequences into clusters. We then apply a "second pass" clade identification algorithm to resolve non-monophyletic groups. We tested our approach with several well-curated protein families (outer membrane porins, acyltransferase, and nuclear receptors) and showed our automated methods recapitulated known subfamilies. We also applied our methods to a broad range of different protein families from multiple databases, including Pfam, PANTHER, and UniProt, and to alignments of RNA viral genomes. Our results showed that AutoPhy rapidly generated monophyletic clusters (subfamilies) within phylogenetic trees evolving at very different rates both within and among phylogenies. The phylogenetic clusters generated by AutoPhy resolved misannotations and identified new protein functional groups and novel viral strains.

Phenotypic diversity analysis of Polygala tenuifolia Willd germplasm resources in China

AbstractPolygala tenuifolia Willd is a perennial herb in the family Polygalaceae and is used as an expectorant and stimulant in traditional Chinese medicine. There is a large demand for P. tenuifolia, while the good cultivars of P. tenuifolia are not enough. In this study, we collected 157 germplasm resources of P. tenuifolia from different regions in China, and 12 phenotypic traits of these samples were analyzed using correlation analysis, principal component analysis (PCA), and cluster analysis methods. The correlation analysis showed the associations between different traits, and the first four principal components contributed 62.63% of the total variation. They contained most of the information of five above-ground traits and eight root traits. Phylogenetic clustering divided materials divided into four taxa, with characteristics of high-yielding specific material, long-rooted specific material, multi-branching specific material, and high plant height specific material, respectively. Our study provides the material and theoretical basis for the utilization of germplasm resources, parental selection, and varietal improvement of P. tenuifolia.

Climatic gradients and forest composition shape bat communities in Eastern Mediterranean pine plantations.

Biotic and abiotic factors can act as filters for determining the species composition of biological communities. We aimed to identify abiotic factors driving the assembly of bat communities in Eastern Mediterranean pine plantations along a north-south climatic gradient, as they are crucial forest habitats for the assessment and conservation of these communities. We expected that bat communities are predominantly shaped by environmental filtering. We conducted acoustic sampling in 35 pine plantations in Israel and analyzed recordings for species identification. We used the ESLTP analysis, an extension of the three-table ordination (RLQ analysis), to explore relationships between environmental characteristics, species occurrences, and functional traits of species while accounting for phylogenetic relationships between species and spatial distribution of the communities. Communities showed phylogenetic and trait clustering. Climatic conditions and forest vegetation composition shaped communities of bats, affecting the distribution of traits related to foraging behaviors, vegetation clutter, and the ability of bats to maneuver in it. Maneuverable species were associated with the northern Mediterranean climatic zone, with a scarce cover of drought-tolerant small shrubs and grassland. Fast flyers were associated with the center-south semi-arid area, with abundant drought-tolerant small shrubs and grassland. These forces might have a predominant role in the assembly of these communities, presumably due to the stressful climatic conditions of the study area. The ESLTP approach can be extended to other taxa and environments to predict species responses to disturbance and environmental changes and give insights into environmental management.

Genome sequence characterization of the unique recombinant vaccine-like lumpy skin disease virus strain Kurgan/2018.

In 2018, the molecular epidemiology of lumpy skin disease in Russia was characterized by a surge in novel recombinant vaccine-like strains causing outbreaks along the southern border, spreading in an easterly direction. Currently, five distinct novel recombinant vaccine-like lineages have been described, designated as clusters 2.1 to 2.5. Based on the complete genome sequence analysis of the causative lumpy skin disease virus (Kurgan/Russia/2018), obtained from an eponymous outbreak, the genome was shown to be composed of a Neethling vaccine strain virus as the dominant parental strain and KSGPO vaccine virus as its minor parental strain. These features are similar to those of Saratov/Russia/2017 and Tyumen/Russia/2018, representing clusters 2.1 and 2.4, respectively. However, Kurgan/Russia/2018 has 16 statistically significant recombination events unique to this sequence, contributing to the phylogenetic clustering of Kurgan/Russia/2018 in yet another cluster designed cluster 2.6, based on analysis involving the complete genome sequences.

Description and genomic characterization of Cohnella caldifontis sp. nov., isolated from hot springs in Yunnan province, south-west China.

A bacterial strain, Gram staining positive, strictly aerobic, rod-shaped, motile bacterium with flagellum and endospore-forming, designated strain YIM B05605T, was isolated from soil sampled in Hamazui hot springs, Tengchong City, Yunnan province, China. Optimum growth for the strain occurred at pH 7.0 and 45°C. MK-7 was the main menaquinone in the strain YIM B05605T. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PME), unidentified glycolipid (GL), three unknown aminophospholipids (APLs) and unidentified polarlipid (PL) were part of the polar lipid profile. The major fatty acids were anteiso-C15:0 and iso-C16:0. The DNA G + C content of the type strain was 58.76%. Genome-based phylogenetic analysis confirmed that strain YIM B05605T formed a distinct phylogenetic cluster within the genus Cohnella. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strain YIM B05605T with the most related species C. fontinalis YT-1101T were 73.42% and 15.7%. Functional analysis by NR, Swiss-prot, Pfam, eggNOG, GO, KEGG databases revealed that strain YIM B05605T has 13 genes related to the sulfur cycle, 2 genes related to the nitrogen cycle. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strain YIM B05605T could be classified as a novel species of the genus Cohnella, for which the name Cohnella caldifontis sp. nov., is proposed. The type strain is YIM B05605T (= CGMCC 1.60052T = KCTC 43462T = NBRC 115921T).

Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone.

The niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron. We split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds' niches converge. Our findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region.

Genome-wide identification and drought stress-induced expression analysis of the NHX gene family in potato.

NHX proteins are transmembrane antiporters belonging to the cation/proton antiporter gene family, with a conserved Na+ (K+)/H+ exchange (PF00999) protein domain. NHXs play a prominent role in plant growth, development, and defense. However, the role of NHX gene family in potato (Solanum tuberosum L.) is yet to be known. In this study, we conducted a genome-wide analysis of the potato NHX gene family. A total of 25 StNHX family members were identified to be unevenly distributed on 10 chromosomes. The proteins ranged in length from 252 to 1,153 amino acids, with molecular masses ranging from 27516.32 to 127860.87 kD, and isoelectric points (pI) ranging from 4.96 to 9.3. Analyses of gene structures and conserved motifs indicated that StNHX genes in the same phylogenetic cluster are conserved. Phylogenetic analysis divided the StNHX genes into three subfamilies (Classes I, II, and III). Synteny analysis indicated that StNHX gene family Class III of NHX and all Arabidopsis thaliana NHXs shared a close evolutionary relationship. Analysis of cis-acting elements in the upstream 1,500bp promoter region of potato NHX genes showed that these genes could be regulated by light, stress, and hormones such as abscisic acid and gibberellic acid. Protein-protein interaction network analysis indicated that StNHX proteins may participate in the regulation of potato growth and stress response. Besides, To determine a potential role of these genes in tissue development and drought response, we analyzed the RNA-seq data of different DM potato tissues. The results showed that NHX genes exhibited distinct tissue-specific expression patterns. We further examined the expression patterns of StNHX in different tissues (leaves, roots, shoots, tubers, stolons, and flowers) during the flowering stage in 'Jizhangshu NO.8.' potato. The qRT-PCR results further confirmed the importance of StNHX genes in potato plant growth and development. We further analyzed the RNA-seq data (DM potato) under different abiotic stresses (salt, drought, and heat), and found that the expression of StNHX genes was induced under abiotic stress. qRT-PCR analysis of shoots and roots of 'Jizhangshu NO.8.' potato treated for 0, 6, 12, and 24h with 15% PEG6000 confirmed that the 25 StNHX genes are involved in the response to drought stress in potato. The results of this study may be useful for selecting appropriate candidate genes for the breeding of new drought-tolerant potato varieties. Furthermore, this study lays a foundation for prospective analysis of StNHX gene functions.

Epidemiological and Molecular Characteristics of Hypermucoviscous and Hypervirulent Klebsiella pneumoniae Isolates in Community Patients in Shanghai, China.

The occurrence and dissemination of hypermucoviscous and hypervirulent Klebsiella pneumoniae (hm-hvKp) isolates in clinical settings are a critical public health problem in the world. However, the data on these isolates in community populations are limited. This study aims to understand the prevalence and molecular characteristics of hm-hvKp isolates in community patients in Shanghai, China. In 2018, an active surveillance system focused on hm-hvKp in community diarrhoeal cases was implemented in Pudong New Area, Shanghai, China, involving 12 sentinel hospitals. The antimicrobial susceptibility of hm-hvKp isolates from fecal samples was tested, and whole-genome sequencing (WGS) was performed to predict the serotypes and sequence types and to identify antimicrobial resistance determinants, virulence determinants, and phylogenetic clusters. The overall prevalence of hm K. pneumoniae isolates was 2.48% (31/1252), with the proportions of 1.76% (22/1252) for hm-hvKp and 0.72% (9/1252) for hm not hv K. pneumoniae. The prevalence of hm-hvKp isolates among different age groups and different months was statistically significant. All the 22 hm-hvKp isolates were susceptible to 20 antimicrobial agents and only carried bla SHV gene, and KL1 and KL2 accounted for eight (36.36%) cases and seven (31.82%) cases, respectively. The eight ST23/KL1 isolates belonged to the predominant CG23-I clade, which typically possessed the virulence determinants profile of rmpA/rmpA2-iro-iuc-ybt-irp-clb. The five ST86/KL2 isolates were assigned to the global clusters ST86/KL2-1 (n=2), ST86/KL2-2 (n=2), ST86/KL2-3 (n=1), all lack of the clb gene. Shanghai ST23/KL1 and ST86/KL2 isolates were closely related to the global isolates from liver abscesses, blood, and urine. Hm-hvKp is carried by the community population of Shanghai, with ST23/KL1 and ST86/KL2 isolates predominant. Hm-hvKp isolates of different continents, different sources, and different virulence levels were closely related. Ongoing surveillance of hm-hvKp isolates in the community population is warranted.

Identification of early flowering mutant gene in Phalaenopsis amabilis (L.) Blume for sgRNA construction in CRISPR/Cas9 genome editing system.

Phalaenopsis amabilis (L.) Blume commonly called Moth Orchid (Orchidaceae) is a natural orchid species designated as the National Flower of Indonesia for its beautiful flower shape and long-lasting flowering period. Basically, P. amabilis has a long vegetative phase that cause late flowering, about 2 to 3 years for flowering, hence a method to shorten vegetative period is desired. The latest technological approach that can be used to accelerate flowering of P. amabilis is the CRISPR/Cas9 genome editing method to inactivate the GAI (Gibberellic Acid Insensitive) gene as a mutant gene that can accelerate the regulation of FLOWERING TIME (FT) genes flowering biosynthesis pathway. The approach that needs to be taken is to silence the GAI gene with a knockout system which begins with identifying and characterizing the GAI target gene in the P. amabilis which will be used as a single guide RNA. CRISPR/Cas9 mediated knockout efficiency is highly dependent on the properties of the sgRNA used. SgRNA consists of a target sequence, determining its specificity performance. We executed phylogenetic clustering for the PaGAI protein with closely related orchid species such as Dendrobium capra, Dendrobium cultivars and Cymbidium sinensis. SWISS-Model as tool webserver for protein structure homology modeling. Results show that P. amabilis has a specific domain with the occurrence of point mutations in the two conservative domains. Therefore, a single guide RNA reconstruction needs to be implemented.

Salmonella Saintpaul outbreak associated with cantaloupe consumption, the United Kingdom and Portugal, September to November 2023.

In September 2023, the UK Health Security Agency identified cases of Salmonella Saintpaul distributed across England, Scotland, and Wales, all with very low genetic diversity. Additional cases were identified in Portugal following an alert raised by the United Kingdom. Ninety-eight cases with a similar genetic sequence were identified, 93 in the United Kingdom and 5 in Portugal, of which 46% were aged under 10years. Cases formed a phylogenetic cluster with a maximum distance of six single nucleotide polymorphisms (SNPs) and average of less than one SNP between isolates. An outbreak investigation was undertaken, including a case-control study. Among the 25 UK cases included in this study, 13 reported blood in stool and 5 were hospitalized. One hundred controls were recruited via a market research panel using frequency matching for age. Multivariable logistic regression analysis of food exposures in cases and controls identified a strong association with cantaloupe consumption (adjusted odds ratio: 14.22; 95% confidence interval: 2.83-71.43; p-value: 0.001). This outbreak, together with other recent national and international incidents, points to an increase in identifications of large outbreaks of Salmonella linked to melon consumption. We recommend detailed questioning and triangulation of information sources to delineate consumption of specific fruit varieties during Salmonella outbreaks.