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The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees
Abstract
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
... Much faster methods exist, but they are generally less accurate [11]. In particular, distance methods (e.g., Neighbor Joining (NJ) [12], BioNJ [13], FastME [14]) build a hierarchical clustering of sequences based on some estimate of their evolutionary pairwise distances, i.e., the sum of the branch lengths along the path between pairs of sequences on the true unobserved phylogenetic tree. NJ is guaranteed to reconstruct the true tree topology if applied to the true distances [15], making the problem of estimating the tree and the set of distances equivalent. ...
... FastTree [62, v2.1.11 SSE3] reconstructs a starting tree using an algorithm inspired from Neighbor-Joining [12] which is subsequently refined with topological rearrangements to optimize the minimum evolution criterion. The tree is then improved using maximum likelihood with NNIs. ...
... computes a distance matrix using Maximum Likelihood, then reconstructs a tree topology using BioNJ [63] and further refines it via topological rearrangements which seek to optimize the Balanced Minimum Evolution score. In virtually all performed experiments we observed that the FastME tree search algorithm led to slightly better performances than the neighbor joining algorithm [12]. We didn't resort to the --gamma option as in our experiments we observed that this lead to worse performances. ...
Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art Maximum likelihood and Bayesian inference methods limits their usability under realistic evolutionary models. Harnessing recent advances in likelihood-free inference and geometric deep learning, we introduce Phyloformer, a fast and accurate method for evolutionary distance estimation and phylogenetic reconstruction. Sampling many trees and sequences under an evolutionary model, we train the network to learn a function that enables predicting the former from the latter. Under a commonly used model of protein sequence evolution and exploiting GPU acceleration, it outpaces fast distance methods while matching maximum likelihood accuracy on simulated and empirical data. Under more complex models, some of which include dependencies between sites, it outperforms other methods. Our results pave the way for the adoption of sophisticated realistic models for phylogenetic inference.
... The evolutionary history was inferred using the Neighbor-Joining method (Saitou and Nei, 1987). The phylogenetic trees were inferred at 1000 bootstrap replicates as described by (Felsenstein, 1985). ...
Trypanosoma evansi is the first hemo-pathogenic trypanosome species of equines and dromedaries. Camels are the principal host of T. evansi; but, horses and other Equidae as well as a large range of other hosts can be infected mechanically. Diagnosis of T. evansi basically relies on conventional Giemsa staining of thin and thick blood smears, which are time consuming and require experienced personnel. Serological test used for parasite detection may suffer the disadvantages in reproducibility due to antigenic variation and significant levels of false negative and false positive results. To overcome the limits of sensitivity and specificity imposed by other diagnostic methods, molecular detection of T. evansi deoxyribonucleic acid (DNA) was carried out in this study on 50 dromedary camels. Five different isolates were obtained from this study. The 5 consensus sequences obtained were compared with other T. evansi isolated from other geographically dispersed locations. The result of this investigation present the first molecular (PCR) detection of T. evansi in camels from Borno and Yobe States of Nigeria and revealed that 5 isolates were identified from this study area which are phylogenetically related to other African isolates from the sub-saharan African, the Middle-East with extension to other parts of Asia and America. This study also revealed two phylogenetically distinct diverse strains base on the ITS-1 gene in the study area. There are no much phylogenetic diversities between the T. evansi strains using the ITS-1 gene. Therefore, it is highly recommended to look into other genes like the RoTat gene and other protein coding genes in order to establish more detailed variations.
... The multiple sequence alignments of wheat miRNAs targeting AvrSr35 gene were conducted by using Clustal Omega program (www.ebi.ac.uk/Tools/msa/clustalo). By using the acquired sequence alignments, evolutionary analysis was performed via MEGA X [24] with adjusted parameters with the neighbor-joining (NJ) method [25], p-distance model [26] and 10,000 repeats of the bootstrap resampling [28]. ...
Wheat (Triticum aestivum L.) belonging to Poaceae family is a valuable staple food all over the world. Puccinia graminis f. sp. tritici is one of the major limiting factor in wheat production, causing stem rust disease. RNA interference (RNAi) is an effective technique for plant production against abiotic stresses. One of the most investigated RNAi molecules is microRNAs (miRNAs). It is well established that miRNAs play important role for the regulation of gene expression at post-transcriptional and pos-translational level. In the present study, wheat miRNAs-stem rust interactions were investigated by in silico methods. For this purpose, reference mature wheat miRNAs were retrieved from miRBase, and the sequences of avirulence gene (AvrSr35) in Puccinia graminis f. sp. tritici were obtained from NCBI. RNAhybrid algorithm was used to predict the relationships between miRNAs and avirulence gene targets. Moreover, a phylogenetic tree was constructed by using miRNAs via MEGA X. We determined that AvrSr35 gene was targeted by a total of 12 miRNAs including tae-miR9657a-3p, tae-miR9671-5p, tae-miR1122c-3p, tae-miR1130b-3p, tae-miR9678-3p, tae-miR9781, tae-miR9666b-3p, tae-miR531, tae-miR9773, tae-miR9778, tae-miR9677b and tae-miR10516. All miRNAs were separated into three major groups. All miRNAs showed close relationship. The first main group consisted of only tae-miR9778. Obtaining findings are expected to contribute roles of miRNAs in the interaction between disease-related miRNAs in plants and pathogens.
... Evolutionary analysis was performed using MEGA 11 as previously described by Tamura et al. (2021). Phylogenetic tree models are constructed using the following three algorithms: maximum likelihood (ML) (Felsenstein 1981), maximum parsimony (MP) (Fitch 1971), and neighbourjoining (NJ) (Saitou and Nei 1987). The bootstrap method was used to test the stability of the phylogenetic tree topology, using 1000 replicates overall. ...
A Gram stain-positive, non-spore-forming, non-motile, short-rod actinomyces strain GXQ1321 T was isolated from maritime surface sediments in Beihai, Guangxi Zhuang Autonomous Region, and a number of categorization studies were performed. Following a period of 72 hours of incubation at a temperature of 30°C within an actinomycetes culture medium, the colony was yellow, circular, smooth, central bulge, convex, opaque, with a 1.8-3.0 mm diameter. Chemotaxonomic studies revealed that the major menaquinone in strain GXQ1321 T is MK-8. The most prevalent cellular fatty acids were anteiso -C 19:0 (27.28%), anteiso -C 15:0 (18.97%), anteiso -C 17:0 (15.95%), and iso -C 16:0 (12.21%). The whole-cell sugars of the strain GXQ1321 T identified were rhamnose, xylose and glucose. Strain GXQ1321 T exhibited the presence of meso-diaminopimelic acid (m-DAP) as a distinctive cell-wall diamino acid, and the polar lipids were identified as diphosphatidylglycerol (DPG), three phosphoglycolipidsone, phosphatidylethanolamine (PE), one unknown phospholipid (UP) and one unknown glycolipid (UG). This strain had 69.6% DNA G + C content. Strain GXQ1321 T is classified as Brevibacterium based on its 16S rRNA gene sequence. It is closely related to Brevibacterium samyangense SST-8 T (96.77%) and Brevibacterium rongguiense 5221 T (96.32%). The results showed that the average nucleotide identity (ANI) values of GXQ1321 T and the above two strain tyoes were 73.91–77.14%, and the digital DNA-DNA hybridisation (dDDH) values were 15.3–21.1%. Based on the phylogenetic, chemotaxonomi and physiologicalc data, strain GXQ1321 T was considered to be a new species of the genus Brevibacterium , named Brevibacterium litoralis sp. nov, with the type strain GXQ1321 T (= MCCC 1K08964 T = KCTC 59167 T ).
... Database search using BLAST The obtained sequence was queried using the NCBI BLASTN 2.9.0+ online database web interface and the sequences were used to construct phylogenetic tree using Mega 6 (Tamura et al., 2013). The evolutionary history was inferred based on Neighbor-Joining method (Saitou and Nei 1987). The obtained sequence was submitted to the GenBank database. ...
... After a final elongation step at 72 °C for 7 min, the resulting patterns obtained were visualized under UV and the results interpreted using GelJ ® software [34]. A similarity matrix, based on Pearson correlation (optimization 1%; position tolerance 1%), was calculated, and the corresponding dendrogram was constructed according to their similarities using the unweighted pair group method with arithmetic averages (UPGMA) [35,36]. ...
Background
The incidence of hospital-acquired infections in extensively drug-resistant Pseudomonas aeruginosa (XDR-PA) has been increasing worldwide and is frequently associated with an increase in mortality and morbidity rates. The aim of this study was to characterize clinical XDR-PA isolates recovered during six months at three different hospitals in Egypt.
Results
Seventy hospital-acquired clinical isolates of P. aeruginosa were classified into multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR), according to their antimicrobial resistance profile. In addition, the possession of genes associated with mobile genetic elements and genes encoding antimicrobial resistance determinants among isolates were detected using polymerase chain reaction. As a result, a significant percentage of the isolates (75.7%) were XDR, while 18.5% were MDR, however only 5.7% of the isolates were non-MDR. The phenotypic detection of carbapenemases, extended-spectrum β-lactamases (ESBLs) and metallo β-lactamase (MBL) enzymes showed that 73.6% of XDR-PA isolates were carbapenemases producers, whereas 75.5% and 88.7% of XDR-PA isolates produced ESBLs and MBL respectively. In addition, PCR screening showed that oxa gene was the most frequently detected gene of carbapenemases (91.4%), while aac(6ʹ)-lb gene was mostly detected (84.3%) among the screened aminoglycosides-resistance genes. Furthermore, the molecular detection of the colistin resistance gene showed that 12.9% of isolates harbored mcr-1 gene. Concerning mobile genetic element markers (intI, traA, tnp513, and merA), intI was the highest detected gene as it was amplified in 67 isolates (95.7%). Finally, phylogenetic and molecular typing of the isolates via ERIC-PCR analysis revealed 10 different ERIC fingerprints.
Conclusion
The present study revealed a high prevalence of XDR-PA in hospital settings which were resistant to a variety of antibiotics due to several mechanisms. In addition, 98% of the XDR-PA clinical isolates contained at least one gene associated with movable genetic elements, which could have aided the evolution of these XDR-PA strains. To reduce spread of drug resistance, judicious use of antimicrobial agents and strict infection control measures are therefore essential.
... jp/ tools-bin/ clust alw). For the phylogenetic tree construction, MEGA X (version 10.1) was utilized using Neighbor joining (NJ) method [23,24]. ...
Background
Autosomal recessive primary microcephaly (MCPH) is a rare neurodevelopmental and genetically heterogeneous disorder, characterized by small cranium size (> − 3 SD below mean) and often results in varying degree of intellectual disability. Thirty genes have been identified for the etiology of this disorder due to its clinical and genetic heterogeneity.
Methods and Results
Here, we report two consanguineous Pakistani families affected with MCPH exhibiting mutation in WDR62 gene. The investigation approach involved Next Generation Sequencing (NGS) gene panel sequencing coupled with linkage analysis followed by validation of identified variants through automated Sanger sequencing and Barcode-Tagged (BT) sequencing. The molecular genetic analysis revealed one novel splice site variant (NM_001083961.2(WDR62):c.1372-1del) in Family A and one known exonic variant NM_001083961.2(WDR62):c.3936dup (p.Val1313Argfs*18) in Family B. Magnetic Resonance Imaging (MRI) scans were also employed to gain insights into the structural architecture of affected individuals. Neurological assessments showed the reduced gyral and sulcal patterns along with normal corpus callosum in affected individuals harboring novel variant. In silico assessments of the identified variants were conducted using different tools to confirm the pathogenicity of these variants. Through In silico analyses, both variants were identified as disease causing and protein modeling of exonic variant indicates subtle conformational alterations in prophesied protein structure.
Conclusion
This study identifies a novel variant (c.1372-1del) and a recurrent pathogenic variant c.3936dup (p.Val1313Argfs*18) in the WDR62 gene among the Pakistani population, expanding the mutation spectrum for MCPH. These findings emphasize the importance of genetic counseling and awareness to reduce consanguinity and address the burden of this disorder.
... Utilizing the full-length multiple sequence alignments and the extracted sequence alignments, distance-based phylogenetic trees were generated using the CLC Main Workbench 22 (QIAGEN) (http://www.clcbio.com/). Phylogenetic trees were constructed using neighbor-joining methods [41], while the evolutionary distances were determined using the Jukes-Cantor model [42]. To determine the reliability of the inferred tree, a bootstrap test was conducted using 1000 replicates. ...
Enterovirus genomic replication initiates at a predicted RNA cloverleaf (5′CL) at the 5′ end of the RNA genome. The 5′CL contains one stem (SA) and three stem-loops (SLB, SLC, SLD). Here, we present an analysis of 5′CL conservation and divergence for 209 human health-related serotypes from the enterovirus genus, including enterovirus and rhinovirus species. Phylogenetic analysis indicates six distinct 5′CL serotypes that only partially correlate with the species definition. Additional findings include that 5′CL sequence conservation is higher between the EV species than between the RV species, the 5′CL of EVA and EVB are nearly identical, and RVC has the lowest 5′CL conservation. Regions of high conservation throughout all species include SA and the loop and nearby bases of SLB, which is consistent with known protein interactions at these sites. In addition to the known protein binding site for the Poly-C binding protein in the loop of SLB, other conserved consecutive cytosines in the stems of SLB and SLC provide additional potential interaction sites that have not yet been explored. Other sites of conservation, including the predicted bulge of SLD and other conserved stem, loop, and junction regions, are more difficult to explain and suggest additional interactions or structural requirements that are not yet fully understood. This more intricate understanding of sequence and structure conservation and variability in the 5′CL may assist in the development of broad-spectrum antivirals against a wide range of enteroviruses, while better defining the range of virus isotypes expected to be affected by a particular antiviral.
... The genetic study was done using Bio-Edit software and NCBI. The evolutionary history was deduced using the Neighbor-joining method (Saitou and Nei, 1987), and the evolutionary distances were calculated using the maximum Composite Likelihood approach (Tamura et al., 2004). ...
Serratia marcescens commonly synthesize a red pigment known as prodigiosin. Prodigiosin is considered a promising pharmaceutical due to its documented properties of having antimicrobial, anticancer, and immunosuppressive effects. This investigation involved the isolation of Serratia marcescens, a bacterium capable of producing prodigiosin, from grey water samples collected in Nnamdi Azikiwe University Awka campus, Nigeria. The central composite design (CCD) of the experiment was applied to generate a set of 31 experimental combinations to study the optimal conditions for pigment production using nutrient broth supplemented with glucose as a fermentation medium. A regression model that described the relationship between the test variables for optimum prodigiosin yield was developed. The regression coefficient (R 2) value of 72.48% implied adequate model fitness. The optimal conditions identified were 24 g/L glucose concentration, pH 7.2, 2.4 mL inoculum size, and 180 rpm agitation speed. A 4.25-fold increase in prodigiosin yield was recorded in optimized condition than in unoptimized condition. Antimicrobial activity against E. coli and Candida albicans shows that prodigiosin has significantly higher activity than the conventional antibiotics tested. Our results indicate that prodigiosin production by Serratia marcescens can be enhanced using statistical models, and the pigment can be an alternative to conventional antibiotics for treating microbial infections.
... In detail, for 5UTR, sequences with a minimum length of 125 nt were used, and for VP1 a minimum of 290. The VP1 and 5′UTR trees were constructed using the neighbor-joining (NJ) method [24], by MEGA 7 [25]. The reliability of the branching orders was assessed by a bootstrap analysis of 1000 replicates [26]. ...
Enteroviruses (EVs) are ubiquitous viruses that circulate worldwide, causing sporadic or epidemic infections, typically during the summer and fall. They cause a broad spectrum of illnesses, ranging from an unspecified febrile clinical presentation to a severe illness. EVs are recognized to be the most frequent etiological agents of aseptic meningitis in children. However, as the infection is usually mild and self-limiting, it remains underestimated, and the epidemiology of EVs is poorly understood. To date, no vaccine or effective therapy for all types of enteroviruses is available, and EVs constitute a public health concern. Here, we investigated the molecular epidemiology of EV strains circulating in the Lazio region over a 10-year time span (2012–2023) by using a sequence-typing approach and phylogenetic analysis. The epidemiological trend of EV infection has undergone changes during the SARS-CoV-2 pandemic (2020–2021), which resulted in a modification in terms of the number of diagnosed cases and seasonality. From 2022, the circulation of EVs showed a behavior typical of the pre-pandemic period, although changes in predominantly circulating strains have been noted. Both epidemic and sporadic circulation events have been characterized in the Lazio region. Further analyses are needed to better characterize any strain with higher potential pathogenic power and to identify possible recombinant strains.
... The resulting partial 16S rRNA gene sequences (varying from 400 to 1,200 nucleotides) were compared to the sequences in the National Center for Biotechnology Information (NCBI) nucleotide database. The evolution history was inferred using the Neighbor-Joining method (Saitou & Nei, 1987). The bootstrap consensus tree inferred from 1,000 replicates is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). ...
In the eastern coastal regions of Odisha, wilt caused by Fusarium oxysporum f. sp. capsici is an extremely damaging disease in chilli. This disease is very difficult to manage with chemical fungicides since it is soil-borne in nature. The natural rhizosphere soil of the chilli plant was used to isolate and test bacterial antagonists for their effectiveness and ability to promote plant growth. Out of the fifty-five isolates isolated from the rhizosphere of healthy chilli plants, five isolates, namely Iso 01, Iso 17, Iso 23, Iso 24, and Iso 32, showed their highly antagonistic activity against F. oxysporum f. sp. capsici under in vitro. In a dual culture, Iso 32 (73.3%) and Iso 24 (71.5%) caused the highest level of pathogen inhibition. In greenhouse trials, artificially inoculated chilli plants treated with Iso 32 (8.8%) and Iso 24 (10.2%) had decreased percent disease incidence (PDI), with percent disease reduction over control of 85.6% and 83.3%, respectively. Iso 32 and Iso 24 treated chilli seeds have shown higher seed vigor index of 973.7 and 948.8, respectively, as compared to untreated control 636.5. Furthermore, both the isolates significantly increased plant height as well as the fresh and dry weight of chilli plants under the rolled paper towel method. Morphological, biochemical, and molecular characterization identified Bacillus amyloliquefaciens (MH491049) as the key antagonist. This study demonstrates that rhizobacteria, specifically Iso 32 and Iso 24, can effectively protect chilli plants against Fusarium wilt while promoting overall plant development. These findings hold promise for sustainable and eco-friendly management of Fusarium wilt in chilli cultivation.
... The sequences obtained in the Sequencing Platform at Fundação Oswaldo Cruz -PDTIS/FIOCRUZ, Brazil, were edited using the Codon-Code Aligner software and compared by BLAST (Basic Local Alignment Search Tool) with sequences available from NCBI / GenBank. Neighbor-joining algorithm of Saitou and Nei [21], with 1000 replicate bootstraps, was used to perform the phylogenetic analysis. ...
Fungal diseases are often linked to poverty, which is associated with poor hygiene and sanitation conditions that have been severely worsened by the COVID-19 pandemic. Moreover, COVID-19 patients are treated with Dexamethasone, a corticosteroid that promotes an immunosuppressive profile, making patients more susceptible to opportunistic fungal infections, such as those caused by Candida species. In this study, we analyzed the prevalence of Candida yeasts in wastewater samples collected to track viral genetic material during the COVID-19 pandemic and identified the yeasts using polyphasic taxonomy. Furthermore, we investigated the production of biofilm and hydrolytic enzymes, which are known virulence factors. Our findings revealed that all Candida species could form biofilms and exhibited moderate hydrolytic enzyme activity. We also proposed a workflow for monitoring wastewater using Colony PCR instead of conventional PCR, as this technique is fast, cost-effective, and reliable. This approach enhances the accurate taxonomic identification of yeasts in environmental samples, contributing to environmental monitoring as part of the One Health approach, which preconizes the monitoring of possible emergent pathogenic microorganisms, including fungi.
... Phaeosclera dematioides CBS:157.81 was used as outgroup. A cladogram was generated by using the Neighbor-Joining method [52] and the evolutionary distances were computed using the Jukes-Cantor method [53]. The analysis was performed with 2000 bootstrap replications. ...
Mal secco is a vascular disease of citrus caused by the mitosporic fungus Plenodomus tracheiphilus. Soil containing infected plant material constitutes an inoculum source for root infections. In this study, the soil bacterial and fungal communities of five lemon orchards located in Syracuse Province (Sicily, Italy) affected by mal secco were analyzed. Soil samples were collected under lemon tree canopies and subjected to total genomic DNA extraction. The fungal DNA was detected through qPCR in all orchards, with variable concentrations. Bacterial and fungal communities were profiled using 16S and ITS amplicon-based high-throughput sequencing, respectively. According to our results, the relative abundances of the most represented bacterial phyla (e.g., Proteobacteria, Actinobacteriota, Acidobacteriota) changed across the orchards, while in the fungal community, the phylum Ascomycota was dominant, with Basidiomycota and Mortierellomycota abundances fluctuating. On the whole, β diversity analysis showed significant variation in the composition of the soil microbial communities across the orchards. This result was confirmed by the analysis of the core community (taxa present at ≥ 75% of total samples), where putative beneficial bacteria resulted in significantly enriched fungus-infected soil samples, suggesting complex microbial interactions. Our findings shed light on the composition and diversity of the soil microbiome in lemon orchards with the occurrence of mal secco infections.
... The antiinflammatory capability of the extract and the isolated metabolites (1-6) were estimated via in vitro inhibition of COX-1 and COX-2. The COX-1 and COX-2 inhibitory study results ( (6) and azelaic acid (4) Figure 2. The evolutionary history was inferred using the Neighbor-Joining method 67 . The bootstrap consensus tree inferred from 500 replicates 68 is taken to represent the evolutionary history of isolated Fusarium solani 68 . ...
Metabolites exploration of the ethyl acetate extract of Fusarium solani culture broth that was isolated from Euphorbia tirucalli root afforded five compounds; 4-hydroxybenzaldehyde (1), 4-hydroxybenzoic acid (2), tyrosol (3), azelaic acid (4), malic acid (5), and fusaric acid (6). Fungal extract as well as its metabolites were evaluated for their anti-inflammatory and anti-hyperpigmentation potential via in vitro cyclooxygenases and tyrosinase inhibition assays, respectively. Azelaic acid (4) exhibited powerful and selective COX-2 inhibition followed by fusaric acid (6) with IC50 values (2.21 ± 0.06 and 4.81 ± 0.14 μM, respectively). As well, azelaic acid (4) had the most impressive tyrosinase inhibitory effect with IC50 value of 8.75 ± 0.18 μM compared to kojic acid (IC50 = 9.27 ± 0.19 μM). Exclusive computational studies of azelaic acid and fusaric acid with COX-2 were in good accord with the in vitro results. Interestingly, this is the first time to investigate and report the potential of compounds 3–6 to inhibit cyclooxygenase enzymes. One of the most invasive forms of skin cancer is melanoma, a molecular docking study using a set of enzymes related to melanoma suggested pirin to be therapeutic target for azelaic acid and fusaric acid as a plausible mechanism for their anti-melanoma activity.
... Briefly, evolutionary history was inferred using the Neighbour-Joining method (Saitou & Nei, 1987). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown below the branches (Felsenstein, 1985). ...
... The study can facilitate the development of bacterial consortia of Fig. 3. The neighborhood-joining method inferred the evolutionary history (Saitou and Nei, 1987). The optimal tree is shown. ...
... The amplification cycles (n = 35) were performed under the following PCR conditions: Initial denaturation at 95 °C for 5 min; Denaturation at 95 °C for 30 s; Annealing at 55 °C for 30 s; Extension at 72 °C for 1 min and Final extension at 72 °C for 10 min. The evolutionary history of both isolates was inferred using the neighbor joining method [27] in MEGA X software [28] and an optimal phylogenetic tree constructed with 1000 bootstrap replicates evaluated the topology. The tree was drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. ...
Co-infection of Lactococcus garvieae and Aeromonas hydrophila, has been confirmed from diseased Nile Tilapia (Oreochromis niloticus), Chithralada strain cultured in a freshwater rearing pond of Alappuzha district of Kerala, India. The aetiological agents behind the disease outbreak were bacteriologically proven and confirmed by 16SrRNA sequencing and phylogenetic analysis. PCR detection of the virulent genes, showed existence of adhesin and hemolysin in L. garvieae and aerolysin in A. hydrophila strain obtained. To fulfil Koch’s postulates, challenge experiments were conducted and median lethal dose (LD50) of L. garvieae and A. hydrophila was calculated as 1 × 105.91 CFU per mL and 1 × 105.2 CFU per mL respectively. Histopathologically, eyes, spleen, and kidney were the predominantly infected organs by L. garvieae and A. hydrophila. Out of the 13 antibiotics tested to check antibiotic susceptibility, L. garvieae showed resistance to almost 7 antibiotics tested, with a resistance to Ciprofloxacin while A. hydrophila was found resistant to Streptomycin and Erythromycin. Understanding the complex interaction between Gram-positive and Gram-negative bacteria in the disease process and pathogenesis in fish host will contribute to efficient treatment strategies. As a preliminary investigation into this complex interaction, the present study is aimed at phenotypic and genotypic characterization, pathogenicity evaluation, and antibiotic susceptibility of the co-infecting pathogens in a diseased sample of freshwater-farmed Nile tilapia.
... China and further aligned by the NCBI-BLAST (https://blast.ncbi.nlm.nih.gov/). In addition, a phylogenetic tree was built using the MEGA 7.0 package (Kumar et al. 2016) with a neighbor-joining approach (Saitou and Nei 1987). ...
Saccharomyces cerevisiae, the primary microorganism involved in ethanol production, is hindered by the accumulation of ethanol, leading to reduced ethanol production. In this study, we employed histidine-modified Fe3O4 nanoparticles (His-Fe3O4) for the first time, to the best of our knowledge, as a method to enhance ethanol yield during the S. cerevisiae fermentation process. The results demonstrated that exposing S. cerevisiae cells to Fe3O4 nanoparticles (Fe3O4 NPs) led to increased cell proliferation and glucose consumption. Moreover, the introduction of His-Fe3O4 significantly boosted ethanol content by 17.3% (p < 0.05) during fermentation. Subsequent findings indicated that the increase in ethanol content was associated with enhanced ethanol tolerance and improved electron transport efficiency. This study provided evidence for the positive effects of His-Fe3O4 on S. cerevisiae cells and proposed a straightforward approach to enhance ethanol production in S. cerevisiae fermentation. The mediation of improved ethanol tolerance offers significant potential in the fermentation and bioenergy sectors.
... The evolutionary history was inferred using the Neighbor-Joining method [19] . The optimal tree is shown. ...
... The study can facilitate the development of bacterial consortia of Fig. 3. The neighborhood-joining method inferred the evolutionary history (Saitou and Nei, 1987). The optimal tree is shown. ...
The poor management process and negligent waste disposal practices from textile and dye industries lead to severe environmental menace. At present, industrial effluent disposal treatment uses physical and chemical approaches. Hence, an investigation was conducted using potent and native microbial isolates from untreated wastewater released from textile industries in the Sanganer area of Jaipur, Rajasthan, India. Eleven competent bacterial strains, which showed potential degradation efficiency, were screened from these two random discharge sites of textile effluent. The study also developed bacterial consortia 1 (DB1-DB7), which showed a maximum of 87%, and consortia 2 (DR1-DR4), which established a minimum decolorization of 65%. The biochemical analysis and 16S rDNA sequencing were investigated, suggesting that potent organisms and their consortium belong to Bacillus and Pseudomonas spp. In the future, the exploitation of these species would scale up for a safe and efficient bioremediation process.
... To construct a neighboring tree, the ClustalW feature was used in the molecular evolutionary genetics analysis (MEGA 11.0.10) (Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan) (Saitou and Nei, 1987). To statistically support the nodes in the phylogenetic trees, bootstrap (1,000 replications) was performed with the alignment threshold value above 80%, and the strain IPR-4 was identified with 93% similarity (Felsenstein, 1985;Tamura et al., 2004). ...
The role of melatonin and plant growth-promoting rhizobacteria (PGPR) in enhancing abiotic stress tolerance has been widely investigated. However, the mechanism underlying the interaction between melatonin and PGPR in drought stress tolerance is poorly understood. In this study, we investigated the role of Bacillus sp. strain IPR-4 co-inoculated with melatonin (IPR-4/MET) to ameliorate drought stress response in soybean. Initially, 16 random isolates were selected from a previously pooled collection of isolates from soil at plant physiology lab and were screened for plant growth promoting (PGP) traits and their survival rate in polyethylene glycol (PEG6000) (5%, 10%, and 15%). Among these isolates Bacillus sp. strain IPR-4 were selected on the base of its significant PGP traits such as the survival rate at gradient concentrations of PEG6000 (15%) compared to other isolates, and production of high levels of indole-3-acetic acid and organic acids, coupled with exopolysaccharide, siderophore, and phosphate solubilization under drought stress. The Bacillus sp. strain IPR-4 were then validated using 16S rRNA sequencing. To further investigate the growth-promoting ability of the Bacillus sp. IPR-4 and its potential interaction with MET, the bacterial inoculum (40 mL of 4.5 × 10 −8 cells/mL) was applied alone or in combination with MET to soybean plants for 5 days. Then, pre-inoculated soybean plants were subjected to drought stress conditions for 9 days by withholding water under greenhouse conditions. Furthermore, when IPR-4/MET was applied to plants subjected to drought stress, a significant increase in plant height (33.3%) and biomass (fresh weight) was observed. Similarly, total chlorophyll content increased by 37.1%, whereas the activity of peroxidase, catalase, ascorbate peroxidase, superoxide dismutase, and glutathione reductase increased by 38.4%, 34.14%, 76.8%, 69.8%, and 31.6%, respectively.
... Based on mutation detection of SNP-labeled data, MEGA X [14] software was used to construct phylogenetic trees for each sample using the Kimura 2-parameter model [15] with neighbor joining [16]. Bootstrap was repeated 1000 times. ...
Objective
The objective of this study was to examine the genetic diversity within and between farmed populations of Onychostoma macrolepis, and to establish a foundation for enhancing the genetic resources of breeding groups through the introduction of new individuals and crossbreeding. A total of 49 individuals were subjected to sequencing using Specific-Locus Amplified Fragment Sequencing (SLAF-seq), one of the restriction site-associated DNA sequencing technologies. The single nucleotide polymorphisms(SNPs)were identified to conduct the analyzation of phylogeny population structure, principal component and genetic diversity.
Results
A total of 853,067 SNPs were identified. The results of the phylogenetic analysis revealed that each sample was genetically clustered into three distinct groups: ZhenPing (ZP), LanGao parents (LG), and their progeny population (LG-F1). Each population was observed to be clustered together. Analysis of population genetic diversity revealed that the observed heterozygosity (Ho) ranged from 0.200 to 0.230, the expected heterozygosity (He) ranged from 0.280 to 0.282, and the polymorphic information content (PIC) ranged from 0.228 to 0.230. These results indicate that the genetic diversity of the population is low and the signs of long-term interbreeding are obvious, but there are differences between the populations, and the genetic diversity of the population can be improved by hybridization in different regions.
... The phylogenetic tree illustrating the variability of analysed mitochondrial DNA fragments was constructed using Mega 11.0.13 software (Tamura, Stecher & Kumar, 2021) and iTOL 6.8.1 (Letunic & Bork, 2021) with the neighbor-joining method (Saitou & Nei, 1987), including 1,000 bootstrap replications. To visualize the connections between all mtDNA HTs of Polish Koniks, the median-joining network (Bandelt, Forster & Röhl, 1999) was constructed in the PopART phylogenetic software (https://popart.maths.otago.ac.nz/, accessed September 2023). ...
Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population's genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performed with the competitive allele-specific PCR genotyping method on 36 horses belonging to all sire lines. The analysis of the mtDNA hypervariable region detected 47 SNPs, which assigned all tested horses to 43 haplotypes. Most dam lines presented more than one haplotype; however, five dam lines were represented by only one haplotype. The haplotypes were classified into six (A, B, E, J, G, R) recognized mtDNA haplogroups, with most horses belonging to haplogroup A, common among Asian horse populations. Y chromosome analysis allocated Polish Koniks in the Crown group, condensing all modern horse breeds, and divided them into three haplotypes clustering with coldblood breeds (28 horses), warmblood breeds (two horses), and Duelmener Pony (six horses). The clustering of all Wicek sire line stallions with Duelmener horses may suggest a historical relationship between the breeds. Additionally, both mtDNA and Y chromosome sequence variability results indicate crossbreeding before the studbooks closure or irregularities in the pedigrees occurred before the DNA testing introduction.
... and then the pairwise comparisons were performed using the NCBI (www.ncbi.nlm.nih.gov) and EzBioCloud databases (www.ezbiocloud.net). Phylogenetic analyses of the two strains and other type species were performed by mega X [12] with three tree-making sets of computer instructions, including the neighbourjoining algorithm [13] with Kimura's two-parameter model [14], the maximum-likelihood algorithm [15] with the Tamura-Nei model and the maximum-parsimony algorithm [16] based on 1000 bootstrap replications. ...
Two Gram-stain-positive, aerobic, oxidase-and catalase-negative, non-motile, and short rod-shaped actinomycetes, named SYSU T00b441 T and SYSU T00b490, were isolated from tidal flat sediment located in Guangdong province, PR China. The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU T00b441 T and SYSU T00b490 were 99.3, 99.5 and 97.1 %, respectively. Strains SYSU T00b441 T and SYSU T00b490 exhibited the highest 16S rRNA gene sequence similarities to Actinotalea ferrariae CF 5-4 T (97.1 %/98.2 %), with ANI values of 74.01/73.88 % and dDDH values of 20.5/20.4 %. In the phylogenomic tree, the two isolates were affiliated with the genus Acti-notalea. The genomes of strains SYSU T00b441 T and SYSU T00b490 were 3.31 and 3.34 Mb, and both had DNA G+C contents of 72.8 mol%, coding 3077 and 3085 CDSs, three and three rRNA genes, and 53 and 51 tRNAs, respectively. Growth occurred at 15-40 °C (optimum, 28-30 °C), pH 4.0-10.0 (optimum, 7.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 3 %). The major fatty acids (>10 %) of strains SYSU T00b441 T and SYSU T00b490 were anteiso-C 15 : 0 and C 16 : 0. The major respiratory quinone was identified as MK-10(H 4). The polar lipids of strains SYSU T00b441 T and SYSU T00b490 were diphosphatidyl glycerol, phos-phatidylglycerol, phosphoglycolipid, phosphatidyl ethanolamine, two phosphatidylinositol mannosides, two glycolipids and two phospholipids. Based on these data, the two strains (SYSU T00b441 T and SYSU T00b490) represent a novel species of the genus Actinotalea, for which the name Actinotalea lenta sp. nov is proposed. The type strain is SYSU T00b441 T (=GDMCC 1.3827 T =KCTC 49943 T).
... Molecular Evolutionary Genetics Analysis version 11 (MEGA 11) was used to construct optimal phylogenetic analysis for accurate species prediction and drawing evolutionary relationships (Tamura et al. 2021). The neighbor-joining method was used to infer the evolutionary history (Saitou and Nei 1987). The evolutionary distances measured in base substitutions per site were calculated using the maximum composite likelihood method (Tamura et al. 2004). ...
Microbes play an essential role in soil fertility by replenishing the nutrients; they encounter various biotic and abiotic stresses disrupting their cellular homeostasis, which expedites activating a conserved signaling pathway for transient over-expression of heat shock proteins (HSPs). In the present study, a versatile soil bacterium Bacillus subtilis strain PSK.A2 was isolated and characterized. Further, the isolated bacterium was exposed with several stresses, viz., heat, salt, acid, alkaline, and antibiotics. Stress-attributed cellular morphological modifications such as swelling, shrinkage, and clump formation were observed under the scanning electron microscope. The comparative protein expression pattern was studied by SDS-PAGE, relative protein stabilization was assessed by protein aggregation assay, and relative survival was mapped by single spot dilution and colony-counting method under control, stressed, lethal, and stressed lethal conditions of the isolate. The findings demonstrated that bacterial stress tolerance was maintained via the activation of various HSPs of molecular weight ranging from 17 to 115 kD to respective stimuli. The treatment of subinhibitory dose of antibiotics not interfering protein synthesis (amoxicillin and ciprofloxacin) resulted in the expression of eight HSPs of molecular weight ranging from 18 to 71 kD. The pre-treatment of short stress dosage showed endured overall tolerance of bacterium to lethal conditions, as evidenced by moderately enhanced total soluble intracellular protein content, better protein stabilization, comparatively over-expressed HSPs, and relatively enhanced cell survival. These findings hold an opportunity for developing novel approaches towards enhancing microbial resilience in a variety of conditions, including industrial bioprocessing, environmental remediation, and infectious disease management.
... Based on the Tamura 3-parameter model, the evolutionary history was estimated using the Maximum Likelihood model [20]. Using the Maximum Composite Likelihood technique [21], neighbour-joining [22], and BioNJ algorithms on pairwise distance matrices, the topology with the highest log likelihood value was chosen to create the trees. The robustness of phylogenetic diversity was evaluated using 1000 bootstrap replicates. ...
Nigeria recorded one of the earliest outbreaks of the Highly Pathogenic Avian Influenza (HPAI) virus H5N1 in 2006, which spread to other African countries. In 2023, 18 countries reported outbreaks of H5N1 in poultry, with human cases documented in Egypt, Nigeria, and Djibouti. There is limited information on the molecular epidemiology of HPAI H5N1 in Nigeria. We determined the molecular epidemiology and genetic evolution of the virus from 2006 to 2021. We investigated the trend and geographical distribution across Nigeria. The evolutionary history of 61 full-length genomes was performed from 13 countries worldwide, and compared with sequences obtained from the early outbreaks in Nigeria up to 2021. MEGA 11 was used to determine the phylogenetic relationships of H5N1 strains, which revealed close ancestry between sequences in Nigeria and those from other African countries. Clade classification was performed using the subspecies classification tool for Bacterial and Viral Bioinformatics Research Center (BV-BRC) version 3.35.5. H5N1 Clade 2.2 was observed in 2006, with 2.3.2, 2.3.2.1f clades observed afterwards and 2.3.4.4b in 2021. Our findings underscore the need for genomics surveillance to track antigenic variation and clades switching to monitor the epidemiological of the virus and safeguard human and animal health.
ImpactsSpecific variations in the hemagglutinin (HA) and neuraminidase (NA) genes of Avian influenza virus are consistent in different geographical regions.
H5N1 Clade 2.2 was reported in 2006, with 2.3.2, 2.3.2.1f afterwards and 2.3.4.4b in 2021.
Nigeria is an epicentre for avian influenza with three major migratory routes for wild birds transversing the country.
It is plausible that the Avian influenza in Northern Nigeria may be linked to wild bird sanctuaries in the region.
... The evolutionary history was inferred by the Neighbor-Joining method [14] using 16S rDNA sequence. The percentage of replicate trees, in which the associated taxa clustered together in the bootstrap test (1000 replicates), was shown next to the branches [15]. ...
Berberine (BBR) is widely used as a botanical pesticide due to its broad-spectrum antibacterial and antifungal activities. However, BBR degradation pathway in soil microorganisms, which determines its impact on soil environment, remains poorly understood. Herein, a novel BBR-degrading bacterium Agrobacterium sp. V1 was isolated and characterized. Agrobacterium sp. V1 was able to utilize BBR as the sole carbon source for cell growth, and 50 μg/mL of BBR was completely degraded within 48 h. To reveal the possible BBR degradation pathway, whole genome sequencing of Agrobacterium sp. V1 was conducted, and proteins in Agrobacterium sp. V1 were aligned with enzymes involved in BBR biosynthesis in Rhizoma Coptidis. The results indicated that more than 60% of enzymes in BBR biosynthesis pathway had orthologs in Agrobacterium sp. V1. Combined with the primary mass spectra of BBR metabolites, a novel BBR degradation pathway in this bacterium was proposed. In summary, the proposed BBR degradation pathway offered new insights into the impact of BBR to the environment and also provided a reference for studying BBR metabolism in microorganisms.
... The taxonomic positions of strain YSY-4.3 were identified by comparing its nucleotide sequence with the nucleotide sequences of 16S rRNA genes in the Genbank/DDBJ/EMBL databases. A phylogenetic tree was computed using MEGA 6.0 [20] and built using the neighborjoining method [21]. ...
This work aimed to isolate and characterize a novel chitin-degrading bacterium from Yok Don National Park, Vietnam, for crop production studies. Among the chitinolytic isolates, strain YSY-4.3 was selected, which grew rapidly and produced a large halo around the colony. 16S rDNA analysis indicated that the strain is a novel species in the genus paenibacillus, and an in vitro evaluation showed that the strain produced phytohormones (IAA, GA3, and zeatin), biofilms, and siderophores; possessed cellulase; and exerted antifungal activity. The whole genome of the strain was 5,628,400 bp with 49.3% GC content, 5056 coding sequences, 48 tRNA, and 1 rRNA. It shared the highest values of digital DNA-DNA hybridization (67.4%) and average nucleotide identity (89.54%) with those of Paenibacillus woosongensis B2_4 (CP126084.1), suggesting a novel species. Of the coding sequences, 4287 proteins were identified by COG, and 2561 were assigned by KEGG. The genome contained at least 51 genes involved in plant growth and resistance to heavy-metal toxicity and 359 carbohydrate-active enzymes. The chitinolytic system of the strain was composed of 15 enzymes, among them, PsChiC, which contained a GH18 catalytic domain and a GH5 catalytic domain, had not been previously reported. In addition, the genome possessed 15 gene clusters encoding antimicrobial metabolites, 10 of which are possible novel clusters. This study expands knowledge regarding novel chitinolytic bacteria from Yok Don National Park and provides a valuable gene resource for future studies.
... The evolutionary distances were calculated using the Kimura two-parameter model [17]. Phylogenetic trees were created using both the neighbour-joining method [18] and the maximum-likelihood method in the mega11 program [19], with bootstrap values based on 1000 replications [20]. ...
A novel bacterial strain, designated as MAH-18 T , was isolated from soil sampled in a flower garden. Cells of strain MAH-18 T were Gram-stain-positive, aerobic, motile, and rod-shaped. The colonies were beige in colour, smooth, and spherical when grown on Reasoner's 2A agar medium. Strain MAH-18 T grew at 20–40 °C, pH 6.0–8.0, and 0–1.0 % NaCl. Cells were able to hydrolyse aesculin, gelatin, and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was determined to be a member of the genus Nocardioides and most closely related to Nocardioides pyridinolyticus OS4 T (97.9 %), Nocardioides hankookensis DS-30 T (97.9 %), Nocardioides aquiterrae GW-9 T (97.6 %), Nocardioides soli mbc-2 T (97.5 %), Nocardioides conyzicola HWE 2-02 T (97.4 %), and Nocardioides mangrovi GBK3QG-3 T (96.3 %). Strain MAH-18 T has a draft genome size of 4 788 325 bp (eight contigs), 4572 protein-coding genes, 46 tRNA, and three rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-18 T and the closest type strains were 81.5–83.4 % and 24.4–25.8 %, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAH-18 T . The G+C content of the genomic DNA of strain was 72.2 mol% and the predominant isoprenoid quinone was MK-8 (H 4 ). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unknown phospholipids. The major cellular fatty acids were determined to be C 16:0 iso and C 17 : 1 ω 6 c . The DNA–DNA hybridization results and phenotypic, genotypic, and chemotaxonomic data demonstrated that strain MAH-18 T represents a novel species, for which the name Nocardioides agri sp. nov. is proposed, with MAH-18 T as the type strain (=KACC 19744 T =CGMCC 1.13656 T ).
... To determine the taxonomic status of ABRV2, a phylogenetic tree was constructed by the maximum-likelihood (ML) method, using the LG + F + I + G substitution model, which yielded the lowest BIC score when tested using MEGA software. Support for the resulting ML tree was inferred by bootstrapping with 1000 replicates [21,22]. The tree was visualized using FigTree (version 1.4.4) ...
The genus Alternaria comprises many important fungal pathogens that infect a wide variety of organisms. In this report, we present the discovery of a new double-stranded RNA (dsRNA) mycovirus called Alternaria botybirnavirus 2 (ABRV2) from a phytopathogenic strain, XC21-21C, of Alternaria sp. isolated from diseased tobacco leaves in China. The ABRV2 genome consists of two dsRNA components, namely dsRNA1 and dsRNA2, with lengths of 6,162 and 5,865 base pairs (bp), respectively. Each of these genomic dsRNAs is monocistronic, encoding hypothetical proteins of 201.6 kDa (P1) and 2193.3 kDa (P2). ABRV2 P1 and P2 share 50.54% and 63.13% amino acid sequence identity with the corresponding proteins encoded by dsRNA1 of Alternaria botybirnavirus 1 (ABRV1). Analysis of its genome organization and phylogenetic analysis revealed that ABRV2 is a new member of the genus Botybirnavirus.
... The unweighted pair group technique with the arithmetic mean (UPGMA) approach was used to conduct the analysis. The greatest composite likelihood approach was used to calculate the evolutionary distances, and the evolutionary history was constructed using the neighbor-joining method [29] with 2000 bootstrap replications, and the internal branches' robustness was evaluated. ...
Bacillus species appearas the most attractive plant growth-promoting rhizobacteria (PGPR) and alternative to synthetic chemical pesticides. The present study examined the antagonistic potential of spore forming-Bacilli isolated from organic farm soil samples of Allahabad, India. Eighty-seven Bacillus strains were isolated and characterized based on their morphological, plant growth promoting traits and molecular characteristics. The diversity analysis used 16S-rDNA, BOX-element, and enterobacterial repetitive intergenic consensus. Two strains, PR30 and PR32, later identified as Bacillus sp., exhibited potent in vitro antagonistic activity against Ralstonia solanaceorum. These isolates produced copious amounts of multiple PGP traits, such as indole-3-acetic acid (40.0 and 54.5 μg/mL), phosphate solubilization index (PSI) (4.4 and 5.3), ammonia, siderophore (3 and 4 cm), and 1-aminocyclopropane-1-carboxylate deaminase (8.1and 9.2 μM/mg//h) and hydrogen cyanide. These isolates were subjected to the antibiotic sensitivity test. The two potent isolates based on the higher antagonistic and the best plant growth-promoting ability were selected for plant growth-promoting response studies in tomatoe, broccoli, and chickpea. In the pot study, Bacillus subtilis (PR30 and PR31) showed significant improvement in seed germination (27–34%), root length (20–50%), shoot length (20–40%), vigor index (50–75%), carotenoid content (0.543–1.733), and lycopene content (2.333–2.646 mg/100 g) in tomato, broccoli, and chickpea. The present study demonstrated the production of multiple plant growth-promoting traits by the isolates and their potential as effective bioinoculants for plant growth promotion and biocontrol of phytopathogens.
... com) and aligned using ClustalW (Thompson et al. 1994) implemented in Molecular Evolutionary Genetics Analysis version 7.0 (MEGA7) for bigger datasets . Using the HVR data, Tsukagoshi et al. (2015) suggested that P. yokohamae and the related species cresthead flounder P. schrenki hybridized primarily in the northern part of the Japanese Archipelago; they found that some P. yokohamae samples were placed in the P. schrenki clade in the neighbor-joining (NJ) tree (Saitou and Nei 1987), and vice versa. Thus, by combining data from Tsukagoshi et al. (2015) deposited in GenBank (acc. ...
The hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae . The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy.
... Acanthomyrmex careoscrobis Mofett, 1986, was used as the outgroup [26]. Te distance-based neighbor joining [27] method was used to infer the relationship between our query sequences and those downloaded from online repositories using the Kimura 2-parameter model [28]and 1000 bootstrap replicates. Analyses were performed with MEGA v7 [29]. ...
The genus Myrmecina was described basing on males of M. graminicola. Though representing the caste type, males were sufficiently described in only two out of 105 species known in the genus. However, the morphology of the male external genitalia remained undescribed. Re-examining by SEM the male of M. graminicola, we describe and illustrate in detail for the first time the external genitalia, redefining and updating the morphological male diagnosis of the genus. We also analyze the overall morphology, illustrating additional peculiar characters of this species as follows: (i) a very distinctive stipital groove in the dorsolateral stipes; (ii) a developed uncinate-shaped mesoscutellar arm; (iii) the antennal cleaning; and (iv) the absence of meso- and metatibial spurs. This morphological study will be useful as a base for further morphological descriptions of the males in other species of the same genus to support correct taxonomic identifications.
... Based on Jaccard similarity matrix, the un-weighted pair group method with arithmetic average (UPGMA) (Sneath and Sokal, 1973) was used to analyze and compare the individual genotypes and generate phenogram using NTSYS-pc version 2.02 (Rohlf, 2000). The neighbor joining (NJ) method (Saitou and Nei, 1987;Studier and Keppler, 1988) was also used to compare individual genotypes and evaluate patterns of genotype clustering using Free Tree 0.9.1.50 software (Pavlicek et al., 1999). ...
The inter simple sequence repeat (ISSR) marker was used in this study for genetic fingerprinting and identification of released chickpea varieties and for the determination of the genetic relationships among these cultivars. A total of 19 released chickpea varieties were subjected to ISSR analysis with the objective of evaluating the genetic diversity among the cultivars. A total of 20 ISSR primers were initially screened and later based on their reproducibility and polymorphism, four of them were selected for the molecular diversity assay. Amplification of genomic DNA of the 19 varieties using four ISSR primers produced 38 scorable fragments. On average, 9.5 polymorphic bands per primer were observed in ISSR analysis. The total number of bands amplified by 3' anchored primers varied from 7 to 12. The primers based on poly (GGAGA) and (AG)YT repeat motifs produced highest number of fragments (10 and 12, respectively), whereas, primers GACA and (GA)T, produced minimum number of fragments (7 and 9, respectively). Overall, 81.58% of the loci were polymorphic and 96.17 and 3.83% of variation were partitioned into within and among population, respectively. The least genetic similarity was recorded between the varieties, Shasho and Minjar (0.41), and highest genetic similarity (0.97) between the varieties, Worku and Kutaye. The UPGMA dendrogram clustered all genotypes into four different clusters and three varieties such as Shasho, Chefe and DZ-10-11 observed to be an out lie. The results indicate the presence of genetic diversity within released cultivars of chickpea in Ethiopia.
... The threshold of homology analysis was set at over 1030 and similarity over 39%. Phylogenetic analysis was performed by ClustalX using the Neighbor-Joining method [31,32]. The hydrophobic N-terminal region was predicted as a transmembrane feature of the enzyme structure using SOSUI [33]. ...
Background
Computational mining of useful enzymes and biosynthesis pathways is a powerful strategy for metabolic engineering. Through systematic exploration of all conceivable combinations of enzyme reactions, including both known compounds and those inferred from the chemical structures of established reactions, we can uncover previously undiscovered enzymatic processes. The application of the novel alternative pathways enables us to improve microbial bioproduction by bypassing or reinforcing metabolic bottlenecks. Benzylisoquinoline alkaloids (BIAs) are a diverse group of plant-derived compounds with important pharmaceutical properties. BIA biosynthesis has developed into a prime example of metabolic engineering and microbial bioproduction. The early bottleneck of BIA production in Escherichia coli consists of 3,4-dihydroxyphenylacetaldehyde (DHPAA) production and conversion to tetrahydropapaveroline (THP). Previous studies have selected monoamine oxidase (MAO) and DHPAA synthase (DHPAAS) to produce DHPAA from dopamine and oxygen; however, both of these enzymes produce toxic hydrogen peroxide as a byproduct.
Results
In the current study, in silico pathway design is applied to relieve the bottleneck of DHPAA production in the synthetic BIA pathway. Specifically, the cytochrome P450 enzyme, tyrosine N-monooxygenase (CYP79), is identified to bypass the established MAO- and DHPAAS-mediated pathways in an alternative arylacetaldoxime route to DHPAA with a peroxide-independent mechanism. The application of this pathway is proposed to result in less formation of toxic byproducts, leading to improved production of reticuline (up to 60 mg/L at the flask scale) when compared with that from the conventional MAO pathway.
Conclusions
This study showed improved reticuline production using the bypass pathway predicted by the M-path computational platform. Reticuline production in E. coli exceeded that of the conventional MAO-mediated pathway. The study provides a clear example of the integration of pathway mining and enzyme design in creating artificial metabolic pathways and suggests further potential applications of this strategy in metabolic engineering.
... After the above optimization procedure, optimizer matrix X was output, which is a denoised and low-rank approximated version of original data Y . Then we calculated the pairwise Euclidean distances between the columns of X, and performed hierarchical clustering (neighbor-joining algorithm) [32] based on the distance matrix. The result was visualized as a phylogenetic tree. ...
Single-cell sequencing has revolutionized our ability to dissect the heterogeneity within tumor populations. In this study, we present LoRA-TV (Low Rank Approximation with Total Variation), a novel method for clustering tumor cells based on the read depth profiles derived from single-cell sequencing data. Traditional analysis pipelines process read depth profiles of each cell individually. By aggregating shared genomic signatures distributed among individual cells using low-rank optimization and robust smoothing, the proposed method enhances clustering performance. Results from analyses of both simulated and real data demonstrate its effectiveness compared with state-of-the-art alternatives, as supported by improvements in the adjusted Rand index and computational efficiency.
... These sequences were compared using DNAMAN 9.0 software, while transmembrane structural domains were analyzed using TMHMM 2.0 software. A phylogenetic tree was constructed by the neighbor-joining method [26,27] using MEGA11 [28,29]. To identify potential miRNAs that might regulate Ae-GRD, the 3' UTR sequence of Ae-GRD was obtained from the NCBI database. ...
iGABAR, a member of the Cys-loop ligand-gated ion channel superfamily, is a significant target of the insecticide ivermectin (IVM). GRD is the potential subunit of the insect iGABAR. However, little information about GRD in Ae. aegypti has been reported. In this study, we involved cloning and characterizing the iGABAR subunit GRD of Ae. aegypti (Ae-GRD). Sequence analysis indicated that Ae-GRD, as part of the cysteine-loop ligand-gated ion channel family, is similar to other insect GRD. RNA interference (RNAi) was employed to explore IVM resistance in Ae. aegypti, resulting in a significant reduction in Ae-GRD expression (p < 0.05), and the mortality of Ae. aegypti adults with Ae-GRD knockdown was significantly decreased after exposure to ivermectin. Bioinformatics prediction identified miR-71-5p as a potential regulator of Ae-GRD. In vitro, dual-luciferase reporter assays confirmed that Ae-GRD expression was regulated by miR-71-5p. Microinjection of miR-71-5p mimics upregulated miR-71-5p expression and downregulated Ae-GRD gene expression, reducing mortality by 34.52% following IVM treatment. Conversely, microinjection of a miR-71-5p inhibitor decreased miR-71-5p expression but did not affect the susceptibility to IVM despite increased Ae-GRD expression (p < 0.05). In conclusion, Ae-GRD, as one of the iGABA receptor subunits, is a potential target of ivermectin. It may influence ivermectin resistance by modulating the GABA signaling pathway. The inhibition of Ae-GRD expression by miR-71-5p decreased ivermectin resistance and consequently lowered the mortality rate of Ae. aegypti mosquitoes. This finding provides empirical evidence of the relationship between Ae-GRD and its miRNA in modulating insecticide resistance, offering novel perspectives for mosquito control strategies.
Lactic acid bacteria (LAB) are naturally found as part of fermented food products and other foodstuff. These organisms are used in the fermentation of vegetables to improve their nutritional value, acceptability, palatability, as well as microbiological qualityand shelf life. Standard microbiological techniques were used to examine 85 different food products for the presence of LAB. The crowded plate approach was used to screen distinct isolates for bacteriocin producing capacity. PCR-based techniques (16S rRNA) were used to identify and characterize lactic acid bacteria associated with food products that have the potential to produce bacteriocins. A total of five hundred and sixty-one (561) lactic acid bacteria were isolated from the food samples of which only 8 (1.42 %) were positive for bacteriocin production. The best five isolates from the 14 with an inhibition zone of 20 mm and more were identified as Lactobacillus plantarum strain PMM09-2528L, Lactobacillus acidophilus strain NK-S10, Lactococcus lactis subsp. lactis strain IFM 63517, Leuconostoc mesenteroides strain M6 and Pediococcus cellicola strain PMM-25. These bacteriocinogenic LAB can be used in the formulation of starter cultures and for commercial use in the biopreservation of vegetables and other food products.
Freshwater crabs (Potamiscus manipuriensis), commonly consumed as local delicacies by the native people in the state of Manipur, were found to harbour metacercariae of Microphallus sp. (Family Microphyllidae), which were morphologically different from metacercariae of Microphallus spp reported earlier from different regions. So, PCR-based molecular characterization of this metacercaria was done utilizing rDNA marker regions: larger subunit (LSU) or 28S (D1-D3 region) and inter-transcribed spacer 2 (ITS2). Sequence and phylogenetic analyses confirmed that the taxon under study belonged to family Microphyllidae of genus Microphallus.
Two Gram-stain-negative, rod-shaped, non-motile, strictly aerobic strains, forming yellow colonies and designated F6058 T and S2608 T , were isolated from marine sediment collected in Weihai, PR China. Both strains grow at 4–40 °C (optimum, 30–33 °C), pH 6.0–7.5 (optimum, pH 6.5) and in the presence of 0–7.0 % (w/v) NaCl. The optimum NaCl concentrations for strains F6058 T and S2608 T were 2.0 % and 2.5 %, respectively. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strains F6058 T and S2608 T share an evolutionary lineage with members of the genus Aequorivita . The isolates exhibited a 16S rRNA gene sequence similarity of 96.7 % to each other. Strains F6058 T exhibited the highest 16S rRNA gene sequence similarity to Aequorivita xiaoshiensis F64183 T (98.8 %), and S2608 T was most similar to Aequorivita capsosiphonis A71 T (96.9 %). Iso-C 15:0 , anteiso-C 15:0 and iso-C 17:0 3-OH were the major fatty acids of strains F6058 T and S2608 T . The sole respiratory quinone of both isolates was menaquinone 6 (MK-6). The polar lipid profiles of the isolates both consisted of phosphatidylethanolamine and phosphoglycolipids; however, strain F6058 T exhibited one glycolipid, one aminolipid and two unidentified polar lipids, and strain S2608 T also had two glycolipids and one unidentified polar lipid. The DNA G+C contents of strains F6058 T and S2608 T were 34.6 % and 37.7 mol%, respectively. Based on their phenotypic, chemotaxonomic and genomic characteristics, strains F6058 T and S2608 T were considered to represent novel species of the genus Aequorivita , for which the names Aequorivita sediminis sp. nov. and Aequorivita marina sp. nov. were proposed. The type strains are F6058 T (=KCTC 92653 T =MCCC 1H01358 T ) and S2608 T (KCTC 92652 T =MCCC 1H01361 T ).
A genome-based polyphasic approach was used to determine the taxonomic status of two novel bacterial strains, SCSIO 12594 T and SCSIO 12813 T , isolated from tissues of a coral. Both strains were Gram-stain-negative and facultatively anaerobic. The genome sizes of strains SCSIO 12594 T and SCSIO 12813 T were 3.9 Mb and 4.1 Mb, respectively, and they possessed DNA G+C contents of 55.1 and 46.2 mol%, respectively . Both strains were found to be catalase- and oxidase-positive, while SCSIO 12594 T also could hydrolyse starch. SCSIO 12594 T was observed to grow at between 20 and 37 °C (optimally at 25 °C) and at a pH range from 6 to 7 and in the presence of 3–7 % (w/v) NaCl. The growth of SCSIO 12813 T required seawater and occurred at 20–30 °C (optimum, 25 °C), pH 5–8 (optimum, pH 6–7) and in the presence of 3–3.7 % (w/v) NaCl. The results of 16S rRNA gene-based phylogenetic analysis indicated that SCSIO 12594 T shared 92.97 % or less sequence similarity with its closest relatives Rhodobium gokarnense JA173 T and other members of the order Hyphomicrobiales . The results of 16S rRNA sequences-based phylogenetic analysis of SCSIO 12813 T indicated that Croceimicrobium hydrocarbonivorans A20-9 T (89.34 %) was the most closely related species. SCSIO 12594 T and SCSIO 12813 T can be readily separated from their closest relatives, as indicated by the results of phylogenomic analysis, low average nucleotide indexes, average amino acid identity, digital DNA–DNA hybridisation (dDDH) similarities and associated phenotypic and chemical data. Consequently, the two coral isolates are considered to represent two novel genera and species for which the names Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov. are proposed, the type strains are SCSIO 12594 T (= JCM 35320 T = GDMCC 1.3060 T ) and SCSIO 12813 T (= JCM 35373 T = GDMCC 1.3063 T ), respectively. In addition, two novel families, Coralliovaceae fam. nov. and Sanyastnellaceae fam. nov are proposed to accommodate Coralliovum pocilloporae gen. nov., sp. nov. and Sanyastnella coralliicola gen. nov., sp. nov., respectively.
Background
Environmental mycobacteria are involved in several infections ranging from lung to skin infections. In Côte d’Ivoire, apart from Mycobacterium ulcerans and Mycobacterium tuberculosis , little information exists on other species. The culture of these species, a real challenge, especially in developing countries like Cote d’Ivoire, limits their identification. However, there are reports in literature of infections caused by these mycobacteria, and few species have never been described in human or animal infections. These are difficult cases to treat because of their resistance to most antituberculosis antibiotics. The aim of our work was to study the diversity of potentially pathogenic mycobacterial species in wastewater drainage channels in different townships and in two hospital effluents in the city of Abidjan.
Methods
Wastewater samples were cultured, followed by conventional polymerase chain reaction (PCR) targeting mycobacterial 16S ribonucleic acid (16S RNA) using PA/MSHA primers. 16 S RNA identified were sequenced by Sanger techniques. Sequences obtained were analyzed, and a phylogenic tree was built.
Results
Fast-growing mycobacteria, including Mycobacterium fortuitum , Mycobacterium phocaicum , Mycobacterium sp., and others presence, were confirmed both by culture and molecular techniques. M. fortuitum strain was the same in effluents of the Treichville University Hospital and in the wastewater of the township of Koumassi. New species never isolated in Côte d’Ivoire, such as M. phocaicum , have been identified in wastewater of the township of Yopougon.
Conclusion
This study showed that the sewer network in the city of Abidjan is colonized by both potentially pathogenic mycobacteria and saprophytic environmental mycobacteria.
Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.
A Gram-stain-negative, orange-yellow, rod-shaped bacterium, designated strain SCSIO 19198 T , was isolated from sediment of the Haima cold seep in the South China Sea, PR China. The strain was aerobic and non-motile. Growth of strain SCSIO 19198 T occurred at pH 7–9 (optimum, pH 7), 15–37 °C (optimum, 25–32 °C) and with 3–8 % (w/v) NaCl (optimum, 3–6 % NaCl). Phylogenetic analyses based on 16S rRNA sequences revealed that strain SCSIO 19198 T belonged to the genus Hwangdonia , having the highest similarity to Hwangdonia seohaensis HD-3 T (98.35 %), followed by Algibacter aquimarinus KYW589 T (95.17 %) and Gelatiniphilus marinus GYP-24 T (94.89 %). The DNA G+C content was 35.92 mol%. The average nucleotide identity value between the genome of strain SCSIO 19198 T and that of H. seohaensis HD-3 T was 88.49 %. The digital DNA–DNA hybridization value between strain SCSIO 19198 T and H. seohaensis HD-3 T was 36 %. The major fatty acids (>10 %) of strain SCSIO 19198 T were iso-C 15 : 0 , iso-C 15 : 1 G, summed feature 3 (C 16 : 1 ω 6 c /C 16 : 1 ω7 c ) and anteiso-C 15 : 0 . MK-6 was the only detected respiratory quinone. The polar lipids of strain SCSIO 19198 T included phosphatidylethanolamine, two aminolipids, glycolipid and two unidentified lipids. The phenotypic, phylogenetic, chemotaxonomic and genomic data clearly suggest that strain SCSIO 19198 T represents a novel species of the genus Hwangdonia , for which the name Hwangdonia lutea sp. nov. is proposed. The type strain is SCSIO 19198 T (=MCCC 1K08674 T =KCTC 102078 T ).
Oyster cultivation is a pivotal economic industry in Hainan Island, South China, where a high oyster species diversity is shown. However, the specific distribution and biodiversity of oyster resources in the island have remained unclear. To elucidate the diversity of oyster species and their distribution there, 307 oyster samples were collected from 29 sites in the intertidal zone around the island, and were identified using both morphological and molecular approaches. A minimum of 12 oyster species were identified in taxonomy, including Crassostrea species (C. gigas angulata, C. sikamea, C. iredalei, C. dianbaiensis, C. talonata, C. ariakensis, and C. hongkongensis), and Saccostrea species (S. malabonensis, S. mordax, S. echinata, S. circumsuta, and S. mordoides). The results revealed a remarkable diversity of oyster species along the coast of the island. Particularly noteworthy are that S. malabonensis and S. mordax constituted 36% and 22% of the collected specimens, respectively. This study provided a comprehensive overview on current state of oyster biodiversity in Hainan, serving as a valuable reference for conservation and research on species distribution and resource dynamics in oyster populations.
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