Phylogenetic Construction Research Articles

An epidemiologic surveillance study based on wastewater and respiratory specimens reveals influenza a virus prevalence and mutations in Taiyuan, China during 2023-2024.

Influenza is a major cause of morbidity and mortality. Influenza A virus (IAV) is one of the most important pathogens causing influenza and often causes global pandemics due to its tendency to mutate. We aim to use epidemiology based on wastewater and respiratory specimens to understand the occurrence of influenza A virus infections in Taiyuan City. A retrospective epidemiology surveillance was carried out at the First Hospital of Shanxi Medical University (FHSMU) and five wastewater treatment plants (WTPs) in Taiyuan city from 2023 to 2024. Reverse transcription real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect influenza A viruses in wastewater and respiratory specimens. High-throughput whole genome sequencing was performed on 17 strains obtained in this study, and subsequent analyses included characterization, phylogenetic construction, amino acid mutation analysis, and antigenic structural variability assessment. 520 wastewater samples and 1,203 throat swab samples were collected. We detected RNA concentration from pH1N1 and H3N2 viruses in wastewater and got 17 genome sequences (5 of pH1N1 and 12 of H3N2) in respiratory specimens. Whole-genome sequencing showed co-prevalence of pH1N1 viruses in the branches of 6B.1A.5a.2a.1 and H3N2 viruses in the branches of 3C.2a1b.2a.2a.3a.a in Taiyuan from 2023 to 2024. Moreover, a HA mutation (N138D), predicted to be of high phenotypic consequence, was found in 8 Taiyuan H3N2 sequences. This study highlights the predominant presence of pH1N1 and H3N2 strains in Taiyuan. The analysis also identified amino acid site variations in the HA antigenic epitopes in H3N2 strains, which may contribute to immune escape.

Phylogenetic and taxonomic revisions of Jurassic sea stars support a delayed evolutionary origin of the Asteriidae.

The superorder Forcipulatacea is a major clade of sea stars with approximately 400 extant species across three orders (Forcipulatida, Brisingida, Zorocallida). Over the past century, the systematics of Forcipulatacea have undergone multiple revisions by various authors, with some considering numerous families such as Asteriidae, Zoroasteridae, Pedicellasteridae, Stichasteridae, Heliasteridae, Labidiasteridae, and Neomorphasteridae, while others recognized only two families (i.e., Asteriidae and Zoroasteridae). Recent molecular analyses have shown the artificial nature of some of these groupings. Notably, four well-supported clades (Zorocallida, Brisingida, Stichasteridae, and Asteriidae) emerged from a synthesis of morphological and molecular evidence. The majority of extinct forcipulatacean species have been placed in modern families. However, many of these fossil species are in need of revision, especially those species placed within the Asteriidae, the largest of all forcipulatacean families. In light of recent advancements in forcipulatacean systematics, we comprehensively reassess six well-preserved Jurassic forcipulatacean taxa, including the earliest crown-group members from the Hettangian (∼201.4 Ma), and also describe two new Jurassic genera, Forbesasterias gen. nov. and Marbleaster gen. nov. We assembled the largest and most comprehensive phylogenetic matrix for this group, sampling 42 fossil and extant forcipulatacean species for 120 morphological characters. To infer phylogenetic relationships and construct an evolutionary timeline for the diversification of major clades, we conducted a Bayesian tip-dating analysis incorporating the fossilized birth-death process. A total of 13 fossil species were sampled in our analysis, including six taxonomically revaluated herein, two recently reappraised species from the Jurassic, and five additional species from the Cretaceous and Miocene. Contrary to prior assumptions, our results indicate that none of the Jurassic taxa investigated belong to Asteriidae or any other modern families, and instead represent stem-forcipulatids. Furthermore, our phylogenetic results suggest that Asteriidae likely originated during the late Cretaceous. Our findings highlight a greater early diversity within the Forcipulatacea than previously presumed, challenging existing perceptions of the evolutionary history of this significant clade of marine invertebrates.

The principle of ecological and molecular consensus in reconstructed plague microbe <i>Yersinia pestis</i> phylogeny

In the second half of the 20th century, through the efforts of scientists from many countries, a coherent theory of natural plague foci (sylvatic plague) was formulated, attempted to describe the history of the origin and evolution of the causative agent of plague infection, the microbeYersinia pestis. But the accumulated knowledge in this regard remained extremely limited. Envisioned by the modern phylogenetics, the methods of phylogenetic constructions in the pregenomic time were rather primitive, “manual”, characteristic of early empirico-intuitive Haeckel phylogenetics. Since the beginning of the 21st century, the introduction of genomic methodologies in the study of the plague pathogen allowed to detail the intraspecific diversity (subspecies, genovariants) of this particularly dangerous pathogen at the level of geographical and local populations (individual natural foci) around the world and to bring the diagnostics and description of intraspecific diversity to a high degree of perfection. Two important discoveries were made. First, the direct ancestor of the plague microbe was reliably established, it turned out to be the causative agent of intestinal infection — Far Eastern scarlet-like fever (Y. pseudotuberculosis0:1b). Secondly, the evolutionary youth of the plague pathogen was shown, the “molecular clock” showed the time of its divergence from the ancestral population no earlier than 30 thousand years ago. Thus, the root of the phylogenetic tree ofY. pestiswas fully characterized. Nevertheless, molecular genetic (MG) achievements do not yet allow to reveal the secrets of its phylogeny, i.e. the origin and sequence of world expansion. The most important reason is the high dependence of the MG of phylogeny reconstructions on the choice of evolutionary model for the analyzed characters: the model of neutral evolution is traditionally accepted, but its adequacy in relation toY. pestisphylogeny is questioned by many well-known ecological (in the broad sense) facts. At the same time, MG achievements contributed to the creation of an ecological (ECO) approach based on the provisions of the theory of natural plague foci in an updated version, according to which the plague pathogen is an evolutionarily young pathogen descended from a psychrophilic pseudotuberculous ancestor. The presumptive ECO scenario has no obvious natural-scientific and historical contradictions and can serve as a null hypothesis for improving the MG methodology of phylogenetic constructions for plague and other similar microbes. It is suggested that the creation of a real phylogeny of the plague microbe is possible only based on integration of MG and ECO approaches.

OHDLF: A Method for Selecting Orthologous Genes for Phylogenetic Construction and Its Application in the Genus Camellia

Accurate phylogenetic tree construction for species without reference genomes often relies on de novo transcriptome assembly to identify single-copy orthologous genes. However, challenges such as whole-genome duplication (WGD), heterozygosity, gene duplication, and loss can hinder the selection of these genes, leading to limited data for constructing reliable species trees. To address these issues, we developed a new analytical pipeline, OHDLF (Orthologous Haploid Duplication and Loss Filter), which filters orthologous genes from transcript data and adapts parameter settings based on genomic characteristics for further phylogenetic tree construction. In this study, we applied OHDLF to the genus Camellia and evaluated its effectiveness in constructing phylogenetic trees. The results highlighted the pipeline’s ability to handle challenges like high heterozygosity and recent gene duplications by selectively retaining genes with a missing rate and merging duplicates with high similarity. This approach ensured the preservation of informative sites and produced a highly supported consensus tree for Camellia. Additionally, we evaluate the accuracy of the OHDLF phylogenetic trees for different species, demonstrating that the OHDLF pipeline provides a flexible and effective method for selecting orthologous genes and constructing accurate phylogenetic trees, adapting to the genomic characteristics of various plant groups.

Production and diversity analysis of cellulases from Anoxybacillus genus

Abstract. Sanjaya RE, Puspaningsih NNT, Rohman A, Rahmasari H, Illias RM, Jantarit N, Fujiyama K, Pratama A, Khairunnisa F. 2024. Production and diversity analysis of cellulases from Anoxybacillus genus. Biodiversitas 25: 2705-2718. Bioconversion of cellulose into sustainable renewable resources of oligosaccharides and glucose requires cellulase action. Genomic sequences of Anoxybacillus cellulases are available in GenBank databases, but no information about their biochemical properties. Anoxybacillus flavithermus TP-01 is a thermophilic, facultatively anaerobic, cellulase-producing bacterium isolated from the mountain of Gunung Pancar hot springs, Bogor, Indonesia. This study aimed to characterize the cellulase produced by Anoxybacillus flavithermus TP-01, a local Indonesian isolate. This cellulase was characterized and the diversity analysis on biochemical properties and structural characteristics was done by in silico approaches. SOPMA, SWISS-MODEL, I-TASSER, ProSA, and SAVES were used for computational analysis on physicochemical characterization, phylogenetic construction, functional analysis, multiple sequence alignment, and secondary-tertiary structure prediction. Physicochemical analysis showed pI<7, indicating acidic property for these proteins. Furthermore, the proteins were thermostable and hydrophilic, as proved by their relatively high aliphatic index and negative GRAVY values. The five sequence motifs harbored a conserved domain of the M42 peptidase/endoglucanase family. Alpha helix was the predominant secondary structure, and the tertiary structure fulfilled the structural quality criteria of QMEAN4, ERRAT, Ramachandran plot, and Z-score. Structural comparison between the template structure and the models revealed significant differences in the loop sections. This study identified a potentially thermostable cellulase of Anoxybacillus flavithermus TP-01, and provided new insights of the physicochemical, functional, and explores the structure-function relationship of cellulase from Anoxybacillus genus based on in silico data.

Identification of Bacterial Diversity in the Magot Digestive System based on 16S rRNA Gene Analysis

The use of feed ingredients has not been addressed until now, in the sense that competition between food and feed is still continuing, especially protein source feed, thus causing a dilemma for farmers.Therefore, in connection with the steps that will be taken in efforts to health livestock and fish farming that will be carried out, efforts are needed in preventing bacterial-based diseases. The purpose of this study was to determine the diversity of all bacteria, both pathogenic and non-pathogenic bacteria found in the magot digestive system using 16S rRNA gene analysis. The results of this study will be a scientific reference for the development of maggot asasafe, effective, and efficient alternative to animal feed.Based on the results of the studies obtained, it can be concluded that the bacteria contained in the digestion of maggots show a diversity of pathogenic and non-pathogenic bacteria, with the form of bacil and cocobacil. Inaddition, DNA extraction and ba cterial identification have also been carried out using the PCR method. The results of the sequencing of the seven bacterial isolates of magot digestive origin showed gooddendograms and nucleotide sequences, so the next stage was bioinformatics analysis and phylogenetic construction, to identify species and their kinship relationships between species.

The chloroplast genomes of two medicinal species (Veronica anagallis-aquatica L. and Veronica undulata Wall.) and its comparative analysis with related Veronica species

Veronica anagallis-aquatica L. and Veronica undulata Wall. are widely used ethnomedicinal plants in China. The two species have different clinical efficacies, while their extremely similar morphology and unclear interspecific relationship make it difficult to accurately identify them, leading to increased instances of mixed usage. This article reports on the complete chloroplast genomes sequence of these two species and their related Veronica species to conduct a comparative genomics analysis and phylogenetic construction. The results showed that the chloroplast (cp) genomes of Veronica exhibited typical circular quadripartite structures, with total lengths of 149,386 to 152,319 base pairs (bp), and GC content of 37.9 to 38.1%, and the number of genes was between 129–134. The total number of simple sequence repeats (SSRs) in V. anagallis-aquatica and V. undulata is 37 and 36, while V. arvensis had the highest total number of 56, predominantly characterized by A/T single bases. The vast majority of long repeat sequence types are forward repeats and palindromic repeats. Selective Ka/Ks values showed that three genes were under positive selection. Sequence differences often occur in the non-coding regions of the large single-copy region (LSC) and small single-copy region (SSC), with the lowest sequence variation in the inverted repeat regions (IR). Seven highly variable regions (trnT-GGU-psbD, rps8-rpl16, trnQ-UUG, trnN-GUU-ndhF, petL, ycf3, and ycf1) were detected, which may be potential molecular markers for identifying V. anagallis-aquatica and V. undulata. The phylogenetic tree indicates that there is a close genetic relationship between the genera Veronica and Neopicrorhiza, and V. anagallis-aquatica and V. undulata are sister groups. The molecular clock analysis results indicate that the divergence time of Veronica may occur at ∼ 9.09 Ma, and the divergence time of these two species occurs at ∼ 0.48 Ma. It is speculated that climate change may be the cause of Veronica species diversity and promote the radiation of the genus. The chloroplast genome data of nine Veronica specie provides important insights into the characteristics and evolution of the chloroplast genome of this genus, as well as the phylogenetic relationships of the genus Veronica.

Relationships between Bitter Taste Receptor Gene Evolution, Diet, and Gene Repertoire in Primates.

Bitter taste perception plays a critical role in deterring animals from consuming harmful and toxic substances. To characterize the evolution of primate Tas2r, test the generality of Tas2r duplication in Cercopithecidae species, and examine whether dietary preferences have shaped the Tas2r repertoire of primate species, we identified Tas2r in the genomes of 35 primate species, including 16 Cercopithecidae, 6 Hominidae, 4 Cebidae, 3 Lemuridae, and 6 other species. The results showed that the total number of primate Tas2r ranged from 27 to 51, concentrating on 2 to 4 scaffolds of each species. Closely related genes were tandemly duplicated in the same scaffold. Phylogenetic construction revealed that Tas2r can be divided into 21 clades, including anthropoid-, Strepsirrhini-, and Cercopithecidae-specific Tas2r duplications. Phylogenetically independent contrast analysis revealed that the number of intact Tas2r significantly correlated with feeding preferences. Altogether, our data support diet as a driver of primate Tas2r evolution, and Cercopithecidae species have developed some specific Tas2r duplication during evolution. These results are probably because most Cercopithecidae species feed on plants containing many toxins, and it is necessary to develop specialized Tas2r to protect them from poisoning.

Epidemiological etiology of Erysiphe sp. and putative viral and phytoplasma-like symptoms in Ayocote bean (Phaseolus coccineus)

Introduction/Objective. Ayocote bean (Phaseolus coccineus) has potential as a source of resistance in breeding programs because it exhibits greater tolerance to plant pathogens than P. vulgaris. However, its sanitary characterization is insipient; therefore, the purpose of this work was to carry out an etiological-epidemiological diagnosis, with emphasis on presumptive symptoms of viral and phytoplasmic organisms, and a typical fungal signs of powdery mildew. Materials and Methods. A plot (50 x 62 m) of flowering Ayocote bean was selected. It was divided into 80 (8 x 10) quadrats (6 x 6 m) and 720 subquadrats (2 x 2 m). From 25 plants with powdery-mildew-type leaf symptoms, mycelium was collected with adhesive tape for light microscopy observation and taxonomic identification. Length-width measurements were made on 60 conidia. Pure mycelium collected in situ and ex situ from 1-5 leaflets/plant was used for genomic analysis by PCR with universal primers ITS1 and ITS4. Samples were sequenced in Macrogen Inc. Korea. A total of 63 plants and 121 trifoliate leaves with viral and phytoplasmic symptoms were collected by direct sampling. In 88/121 samples, genomic analysis was performed by PCR with universal primers for Potyvirus (1), Begomovirus (2), and Phytoplasmas (1). Sequence editing and analysis were performed in SeqAssem and BLASTn/GenBank. Phylogenetic constructions were developed in Mega 11 with MUSCLE, Maximum Likelihood (ML), and HKY substitution model (1000-Bootstrap). Putative powdery mildew severity (%), flower damage (%), Macrodactylus sp. adult density, and plant vigor (%) were evaluated in 80 quadrats (3subquadrats/quadrat) with App-Monitor®v1.1 configured with a 5-class scale. In GoldenSurfer® v10, Kriging geostatistical analysis was performed to determine the spatial interrelationship between these variables. Results. Erysiphe vignae was identified as associated with powdery mildew of P. coccineus. The fungus, with hyaline, ovoid to ellipsoid conidia measuring 31.74 ± 0.3419 μm x 15.11 ± 0.1579 μm, without the presence of fibrosin bodies, had 100% genomic homology. This is the first report in Mexico. With average July-August temperature and relative humidity of 16.3 °C (±5.8) and 92.8 % (±10.7), respectively, powdery mildew leaf incidence and severity were 65.3 and 22.7 % (±16.9, range: 0 - 66.5 %), respectively. The most inductive focus (60-80 % severity) had an aggregate e 4-quadrat pattern (96 m2, lag = 4 and σ2-s = 450). Inoculum dispersal was significantly associated with dominant North-South winds and plant vigor (lag = 4 and σ2-s = 470). Flower damage was inconclusive in its spatial association with powdery mildew and Macrodactylus sp. suggesting uncorrelated events. No Potyvirus, Begomovirus, or Phytoplasmas were detected associated with yellowing, leaf distortion, mosaic, internode shortening, and other symptoms observed in situ. This confirms the relative tolerance/resistance reported for P. coccineus. Conclusion. E. vignae (Erysiphales: Erysiphaceae) associated with P. coccineus is reported for the first time in Mexico with moderate to intense epidemic level, which indicates its susceptible condition to this fungus. However, negative results for Potyvirus, Begomovirus, and Phytoplasmas, validate the apparent tolerance/resistance of P. coccineus to these organisms.

Molecular phylogenetics of the Ophiocordyceps sinensis-species complex lineage (Ascomycota, Hypocreales), with the discovery of new species and predictions of species distribution

Ophiocordyceps sinensis is a famous traditional Chinese medicine adapted to the alpine environment of the Qinghai-Tibet Plateau and adjacent regions. Clarification of the species diversity of Ophiocordyceps sinensis and its relatives could expand the traditional medicinal resources and provide insights into the speciation and adaptation. The study is prompted by the discovery of a new species, O. megala, described here from a biodiversity hotspot in the Hengduan Mountains, China. Combined morphological, ecological, and phylogenetic evidence supports its distinctiveness from O. sinensis, O. xuefengensis, and O. macroacicularis. Additionally, based on the phylogenetic construction of Ophiocordyceps, a special clade was focused phylogenetically on the more closely related O. sinensis complex, which was defined as the O. sinensis- species complex lineage. A total of 10 species were currently confirmed in this lineage. We made a comprehensive comparison of the sexual/asexual morphological structures among this species complex, distinguishing their common and distinctive features. Furthermore, using the method of species distribution modelling, we studied the species ocurrences in relation to climatic, edaphic, and altitudinal variables for the eight species in the O. sinensis-species complex, and determined that their potential distribution could extend from the southeastern Qinghai-Tibet Plateau to the Xuefeng Mountains without isolating barrier. Thus, the biodiversity corridor hypothesis was proposed around the O. sinensis-species complex. Our study highlights the phylogeny, species diversity, and suitable distribution of the O. sinensis-species complex lineage, which should have a positive implication for the resource discovery and adaptive evolution of this unique and valuable group.

Comparative analyses of complete chloroplast genomes reveal interspecific difference and intraspecific variation of Tripterygium genus.

The genus Tripterygium was of great medicinal value and attracted much attention on the taxonomic study using morphological and molecular methods. In this study, we assembled 12 chloroplast genomes of Tripterygium to reveal interspecific difference and intraspecific variation. The sequence length (156,692-157,061 bp) and structure of Tripterygium were conserved. Comparative analyses presented abundant variable regions for further study. Meanwhile, we determined the ndhB gene under positive selection through adaptive evolution analysis. And the phylogenetic analyses based on 15 chloroplast genomes supported the monophyly of Tripterygium hypoglaucum and the potential sister relationship between Tripterygium wilfordii and Tripterygium regelii. Molecular dating analysis indicated that the divergence time within Tripterygium was approximately 5.99 Ma (95% HPD = 3.11-8.68 Ma). The results in our study provided new insights into the taxonomy, evolution process, and phylogenetic construction of Tripterygium using complete plastid genomes.

Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae).

Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analyzed repeat dynamics, and identified potential hybridization events within the genus. Our analysis confirmed the presence of four major infrageneric clades (A-D) within Amomum, with clades A-C exclusively comprising diploid species (2n = 48) and clade D encompassing both diploid and tetraploid species (2n = 48 and 96). We observed an increase in the repeat content within the genus, ranging from 84% to 89%, compared to outgroup species with 75% of the repeatome. The SIRE lineage of the Ty1-Copia repeat superfamily was prevalent in most analyzed ingroup genomes. We identified significant difference in repeatome structure between the basal Amomum clades (A, B, C) and the most diverged clade D. Our investigation revealed evidence of ancient hybridization events within Amomum, coinciding with a substantial proliferation of multiple repeat groups. This finding supports the hypothesis that ancient hybridization is a driving force in the genomic evolution of Amomum. Furthermore, we contextualize our findings within the broader context of genome size variations and repeatome dynamics observed across major monocot lineages. This study enhances our understanding of evolutionary processes within monocots by highlighting the crucial roles of repetitive elements in shaping genome size and suggesting the mechanisms that drive these changes.

Isolation and molecular detection of endophytic actinomycetes Nocardiopsis dassonvillei DMS 1 (MH900216) from marine sea grasses with bacterial inactivation

In recent years, new antibiotics have been discovered around the world in order to inhibit multi-drug resistant (MDR) pathogens. To overcome this problem, marine actinomycetes are an alternative choice for producing new bioactive compounds that inhibit MDR bacteria. The typical endophytic actinomycete (EA) Nocardiopsis dassonvillei (N. dassonvillei) DMS 1 (MH900216) was isolated from marine Sea grasses by surface sterilization method. After surface sterilization, it was confirmed that the pure, dry, white-colored spore producing colonies emerged from the internal tissue of the Sea grasses. The crude extract of N. dassonvillei DMS 1 (MH900216) demonstrated 8- and 10-mm zones of inhibition against A. baumannii and K. pneumoniae, respectively. The composition of N. dassonvillei DMS 1 (MH900216) with potential anti-bacterial properties was studied by GC-MS analysis and exhibited 22 chemical compounds. Subsequently, the molecular identification and phylogenetic construction of the isolated EA strain was confirmed as N. dassonvillei DMS 1 (MH900216). The liquid-liquid extraction of the compound demonstrated 24- and 26-mm zones of inhibition against A. baumannii and K. pneumoniae, respectively. Furthermore, the purified crude compound demonstrated 92% and 94% cell death against A. baumannii and K. pneumoniae, respectively, at a minimum inhibitory concentration of 500 μg/mL. Overall, the present study demonstrated the antibacterial properties of the EA N. dassonvillei DMS 1 (MH900216) isolated from Sea grasses and their importance as alternative sources for discovering new antibiotics to inhibit MDR bacteria.

An evolution strategy approach for the balanced minimum evolution problem.

The Balanced Minimum Evolution (BME) is a powerful distance based phylogenetic estimation model introduced by Desper and Gascuel and nowadays implemented in popular tools for phylogenetic analyses. It was proven to be computationally less demanding than more sophisticated estimation methods, e.g. maximum likelihood or Bayesian inference while preserving the statistical consistency and the ability to run with almost any kind of data for which a dissimilarity measure is available. BME can be stated in terms of a nonlinear non-convex combinatorial optimization problem, usually referred to as the Balanced Minimum Evolution Problem (BMEP). Currently, the state-of-the-art among approximate methods for the BMEP is represented by FastME (version 2.0), a software which implements several deterministic phylogenetic construction heuristics combined with a local search on specific neighbourhoods derived by classical topological tree rearrangements. These combinations, however, may not guarantee convergence to close-to-optimal solutions to the problem due to the lack of solution space exploration, a phenomenon which is exacerbated when tackling molecular datasets characterized by a large number of taxa. To overcome such convergence issues, in this article, we propose a novel metaheuristic, named PhyloES, which exploits the combination of an exploration phase based on Evolution Strategies, a special type of evolutionary algorithm, with a refinement phase based on two local search algorithms. Extensive computational experiments show that PhyloES consistently outperforms FastME, especially when tackling larger datasets, providing solutions characterized by a shorter tree length but also significantly different from the topological perspective. The software and the data are available at https://github.com/andygaspar/PHYLOES.

<i>In Silico</i> Analysis of <i>Phalaenopsis Orchid Homeobox1</i> (<i>POH1</i>) Functional Gene for Shoot Development in <i>Phalaenopsis</i> Orchid

The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved. Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11.

Molecular characterization of Tapah fish (Wallago leerii, Bleeker 1851) from Riau Province based on Cytochrome b gen

Tapah fish (Wallago leerii) is a fish with high economic value in Riau Province. Molecular research on W. leerii is very important to do. This study aims to determine the molecular characteristics of W. leerii from Riau Province based on the Cytochrome b gene. The universal primer Cytochrome b is used for the Polymerase Chain Reaction (PCR) process. The PCR result is a partial Cytochrome b gene with a length of 373 bp. Multiple alignments were performed on nucleotide sequences of the Cytochrome b gene of W. leerii from river of Tapung and Indragiri Riau with the cytochrome b gene of other fish from Genbank and analyzed using the MEGA program version 6.0. Phylogenetic construction using the Cytochrome b gene can distinguish W. leerii from river of Tapung and Indragiri Riau, with other species.Keywords:AlignmentsMolecularGenBank

Fungal taxonomy: A puzzle with many missing pieces

Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.

Genetic characterization and whole-genome sequencing-based genetic analysis of influenza virus in Jining City during 2021-2022.

The influenza virus poses a significant threat to global public health due to its high mutation rate. Continuous surveillance, development of new vaccines, and public health measures are crucial in managing and mitigating the impact of influenza outbreaks. Nasal swabs were collected from individuals with influenza-like symptoms in Jining City during 2021-2022. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect influenza A viruses, followed by isolation using MDCK cells. Additionally, nucleic acid detection was performed to identify influenza A H1N1, seasonal H3N2, B/Victoria, and B/Yamagata strains. Whole-genome sequencing was conducted on 24 influenza virus strains, and subsequent analyses included characterization, phylogenetic construction, mutation analysis, and assessment of nucleotide diversity. A total of 1,543 throat swab samples were collected. The study revealed the dominance of the B/Victoria influenza virus in Jining during 2021-2022. Whole-genome sequencing showed co-prevalence of B/Victoria influenza viruses in the branches of Victoria clade 1A.3a.1 and Victoria clade 1A.3a.2, with a higher incidence observed in winter and spring. Comparative analysis demonstrated lower similarity in the HA, MP, and PB2 gene segments of the 24 sequenced influenza virus strains compared to the Northern Hemisphere vaccine strain B/Washington/02/2019. Mutations were identified in all antigenic epitopes of the HA protein at R133G, N150K, and N197D, and the 17-sequence antigenic epitopes exhibited more than 4 amino acid variation sites, resulting in antigenic drift. Moreover, one sequence had a D197N mutation in the NA protein, while seven sequences had a K338R mutation in the PA protein. This study highlights the predominant presence of B/Victoria influenza strain in Jining from 2021 to 2022. The analysis also identified amino acid site variations in the antigenic epitopes, contributing to antigenic drift.

Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing

Bacteria containing the enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD+) can reduce plant ethylene levels and increase root development and elongation resulting in increased resiliency to drought and other plant stressors. Although these bacteria are ubiquitous in the soil, non-culture-based methods for their enumeration and identification are not well developed. In this study we compare two culture-independent approaches for identifying ACCD+ bacteria. First, quantitative PCR (qPCR) and direct acdS sequencing with newly designed gene-specific primers; and second, phylogenetic construction of 16S rRNA amplicon libraries with the PICRUSt2 tool. Using soils from eastern Colorado, we showed complementary yet differing results in ACCD+ abundance and community structure responding to water availability. Across all sites, gene abundances estimated from qPCR with the acdS gene-specific primers and phylogenetic reconstruction using PICRUSt2 were significantly correlated. However, PICRUSt2 identified members of the Acidobacteria, Proteobacteria, and Bacteroidetes phyla (now known as Acidobacteriota, Pseudomonadota, and Bacteroidota according to the International Code of Nomenclature of Prokaryotes) as ACCD+ bacteria, whereas the acdS primers amplified only members of the Proteobacteria phyla. Despite these differences, both measures showed that bacterial abundance of ACCD+ decreased as soil water content decreased along a potential evapotranspiration (PET) gradient at three sites in eastern Colorado. One major advantage of using 16S sequencing and PICRUSt2 in metagenomic studies is the ability to get a potential functional profile of all known KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes within the bacterial community of a single soil sample. The 16S-PICRUSt2 method paints a broader picture of the biological and biochemical function of the soil microbiome compared to direct acdS sequencing; however, phylogenetic analysis based on 16S gene relatedness may not reflect that of the functional gene of interest.

Phylogenetic construction of Green Algae Based on the rbcL Gene

Phylogenetic construction of Green Algae Based on the rbcL Gene