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A globally implemented unified phylogenetic classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. We formulated global consensus of HRSV classification on the basis of the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality curated dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to GenBank and GISAID (https://www.gisaid.org) public sequence databases through March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B and provided guidelines for defining prospective lineages. Our classification demonstrated robustness in its applicability to both complete and partial genomes. We envision that this unified HRSV classification proposal will strengthen HRSV molecular epidemiology on a global scale.

Eight porcine parvovirus (PPV) species, designated as PPV1 through PPV8, have been identified in swine. Despite their similarities, knowledge about their distribution and genetic differences remains limited, resulting in a gap in the genetic classification of these viruses. In this study, we conducted a comprehensive analysis using PPV1 to PPV7 genome sequences from Colombia and others available in the GenBank database to propose a classification scheme for all PPVs. Sera from 234 gilts aged 180 to 200 days were collected from 40 herds in Colombia. Individual detection of each PPV (PPV1 through PPV7) was performed using end-point PCR. Complete nucleotide (nt) sequencing was performed on the PPV1 viral protein (VP), and near-complete genome (NCG) sequencing was carried out for novel porcine parvoviruses (nPPVs) (PPV2 through PPV7). Phylogenetic analyses were conducted by comparing PPV1-VP sequences to 94 available sequences and nPPVs with 565 NCG, 846 nPPV-VP, and 667 nPPV–nonstructural protein (NS) sequences. Bayesian phylogenetic analysis was used to estimate substitution rates and the time to the most recent common ancestor for each PPV. The highest prevalence was detected for PPV3 (40.1%), followed by PPV5 (20.5%), PPV6 (17%), PPV1 (14.5%), PPV2 (9.8%), PPV4 (4.2%), and PPV7 (1.3%). Notably, all tested sera were negative for PPV8 genomes. An analysis of the PPV1-VP sequences revealed two main clades (PPV1-I and PPV1-II), with the sequences recovered in this study grouped in the PPV1-II clade. Comparative analysis showed significant genetic distances for PPV2 to PPV7 at the NCG (>6.5%), NS (>6.3%), and VP (>7.5%) regions, particularly when compared to equivalent regions of PPV genomes recovered worldwide. This study highlights the endemic circulation of nPPVs in Colombian pig herds, specifically among gilts. Additionally, it contributes to the phylogenetic classification and evolutionary studies of these viruses. The proposed method aims to categorize and divide subtypes based on current knowledge and the genomes available in databanks.

The polygrammoid fern family Polypodiaceae represents one of the most diversified epiphytic fern groups, with more than 1600 species distributed on all continents except Antarctica, with the highest species diversity in tropical and subtropical regions. Despite progress in recent phylogenetic studies of Polypodiaceae, the infrafamilial classification of this group of ferns is still problematic. Here, we explore the phylogenetic relationship within Polypodiaceae using plastid genome (plastome) and nuclear ribosomal cistron genome data obtained from high-throughput sequencing. Although genome skimming data strongly support the monophyly of many genera and clades of Polypodiaceae, relationships within some clades and along the backbone of the phylogeny remain incongruent between plastome and nuclear data. The explanation is possibly a factor of complex evolutionary history found in these clades, such as rapid radiation, incomplete lineage sorting, ancient hybridization, and recent introgression. Based on the concatenated dataset, our phylogenetic analyses support nine major clades in Polypodiaceae, which merit the recognition as subfamilies, Crypsinoideae, Grammitidoideae, Loxogrammoideae, Microsoroideae, Platycerioideae, Polypodioideae, Adetogrammoideae, Campyloneuroideae, and Serpocauloideae, while the latter three are separated from Polypodioideae as new subfamilies. All of these infrafamilial divisions, identified with molecular data, are further supported by non-molecular features including leaf dissection, venation, scales and paraphyses, soral features, and geographical distributions. Systematic and taxonomic discussions on the subfamilial treatment are also provided.

Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomie communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.

Intestinal bacteria in healthy humans and animals are important reservoirs of antimicrobial resistance (AMR) genes. Certain Escherichia coli lineages dominate the global spread of AMR, but the extent of their host specificity and its impact on transmission remains unclear. Here, 1,198 E. coli isolates from cattle, chickens, humans, and pigs across Germany, the UK, Spain, and Vietnam were classified for host-association using a phylogeny-based bioinformatic approach, with non-host-associated isolates defined as ‘generalists’. To validate this classification, 17 extended-spectrum beta-lactamase (ESBL)-producing isolates representing host-associated or generalist clusters were administered as a cocktail to three groups of weaner pigs, either untreated or treated with amoxicillin or ceftiofur. Bacterial shedding was monitored via culture and isolate-specific PCR up to 56 days post-inoculation. Colonization occurred within 24 h, with shedding peaking early and declining over time. Only 12 of 17 isolates were recovered post-inoculation; four were persistently detected, including one pig-associated, one bovine, one chicken, and one generalist isolate. These findings suggest limitations in the classification approach, possible low host selectivity in pigs, and/or incomplete knowledge of colonization mechanisms. Nonetheless, the model successfully identified isolates capable of stable colonization, supporting its utility for studying AMR E. coli host adaptation.

Soybean ( Glycine max ) is a pivotal oilseed crop that is particularly vulnerable to unfavorable environmental conditions. The HVA22 gene family, known for the TB2/DP1/HVA22 domain, plays a crucial role in stress response across plants. Despite their significance, a thorough genome-wide analysis of the HVA22 family in soybean has not been conducted. In this study, we initially report the identification and chromosomal mapping of forty GmHVA22 genes, which encode the conserved TB2/DP1/HVA22 domain and are predominantly located in transmembrane regions. Phylogenetic analysis revealed that all the GmHVA22 genes are distributed into six distinct subgroups, showing close phylogenetic relationships with HVA22 genes from other species. The gene structures within each subgroup were found to be relatively conserved, whereas significant variations were observed among GmHVA22 genes from different subgroups. Cis-element analysis revealed that most GmHVA22 genes harbor elements pivotal for plant growth and development, especially the Box-4 and G-box motifs. Furthermore, the expression profiles of the majority of GmHVA22 genes were responsive to abscisic acid (ABA) and various abiotic stress treatments, suggesting their potential functions in ABA-mediated abiotic stress responses in soybean. Notably, the pronounced upregulation of six specific GmHVA22 genes ( GmHVA22a1 , GmHVA22b1 , GmHVA22b5 , GmHVA22k1 , GmHVA22n1 , and GmHVA22r3 ) under drought stress conditions implicates them in soybean’s drought tolerance mechanisms. These findings underscore the potential roles of GmHVA22s in ABA signaling and drought stress tolerance, as well as their participation in the regulation of plant growth and developmental processes.

The Golden 2-Like (G2-like or GLK) transcription factors are essential for plant growth, development, and many stress responses as well as heavy metal stress. However, G2-like regulatory genes have not been studied in soybean. This study identified the genes for 130 G2-Like candidates’ in the genome of Glycine max (soybean). These GLK genes were located on all 20 chromosomes, and several of them were segmentally duplicated. Most GLK family proteins are highly conserved in Arabidopsis and soybean and were classified into five major groups based on phylogenetic analysis. These GmGLK gene promoters share cis-acting elements involved in plant responses to abscisic acid, methyl jasmonate, auxin signaling, low temperature, and biotic and abiotic stresses. RNA-seq expression data revealed that the GLK genes were classified into 12 major groups and differentially expressed in different tissues or organs. The co-expression network complex revealed that the GmGLK genes encode proteins involved in the interaction of genes related to chlorophyll biosynthesis, circadian rhythms, and flowering regulation. Real-time quantitative PCR analysis confirmed the expression profiles of eight GLK genes in response to cadmium (Cd) and copper (Cu) stress, with some GLK genes significantly induced by both Cd and Cu stress treatments, implying a functional role in defense responsiveness. Thus, we present a comprehensive perspective of the GLK genes in soybean and emphasize their important role in crop development and metal ion stresses.

Premise of research. Phylogenetic analyses have shown that tribe Melastomateae is biphyletic, consisting of two nonsister clades, the core Melastomateae and the Marcetia alliance, both supported by molecular and morphological characters. Methodology. In this study, we describe the new tribe Marcetieae and revise its generic limits based on a molecular phylogeny and a reevaluation of morphological characters. A short description; notes on distribution, habitat, and taxonomy; and a list of species plus an identification key are presented for all accepted genera. Pivotal results. We propose the recognition of 19 genera in this tribe, including a new genus (Rostranthera) and the resurrection of Dicrananthera, Leiostegia, Noterophila, and Pseudoernestia. Conclusions. Ernestia and Macairea were not fully resolved either in the molecular phylogeny or morphologically, and these genera need additional sampling of taxa and molecular markers to define their generic limits.

Inoculation with Rhizobium can improve not only host yield and quality but also host adaptability to stress. The match between inoculated strains and hosts and resistance to stress are the key factors determining the inoculation effect. Four types of Desmodium, Pleurolobus gangeticus, Puhuaea sequax, Grona heterocarpos, and Polhillides velutina, were used to capture Rhizobium strains in soil, and the phylogenetic classification and salt and acid—alkaline resistances of the strains were determined through isolation, identification, and different salt and pH treatments. The phylogenetic classification of the 62 rhizobial strains was determined by 16S rDNA analysis. After comparison, the strains were grouped into 10 groups with known strains of rhizobia, including 14 strains of fast-growing rhizobia grouped with Rhizobium tropici and Rhizobium oryzicola and 48 strains of slow-growing rhizobia. The salt tolerance and acid—base adaptability of 52 strains were qualitatively and quantitatively determined in this study, and salt stress was found to have varying effects on the growth of different strains. Some strains grew normally on media with NaCl concentrations of 0.4 and 0.35 mol/L and had strong salt tolerance. The plants grew normally on media with pH 5–9. This study provides theoretical support for the classification of Desmodium and provides efficient Rhizobium strains for the cultivation and application of Desmodium.

Background The genus Helicobacter are gram-negative, microaerobic, flagellated, mucus-inhabiting bacteria associated with gastrointestinal inflammation and classified as gastric or enterohepatic Helicobacter species (EHS) according to host species and colonization niche. While there are over 30 official species, little is known about the physiology and pathogenic mechanisms of EHS, which account for most in the genus, as well as what genetic factors differentiate gastric versus EHS, given they inhabit different hosts and colonization niches. The objective of this study was to perform a whole-genus comparative analysis of over 100 gastric versus EHS genomes in order to identify genetic determinants that distinguish these Helicobacter species and provide insights about their evolution/adaptation to different hosts, colonization niches, and mechanisms of virulence. Results Whole-genome phylogeny organized Helicobacter species according to their presumed gastric or EHS classification. Analysis of orthologs revealed substantial heterogeneity in physiological and virulence-related genes between gastric and EHS genomes. Metabolic reconstruction predicted that unlike gastric species, EHS appear asaccharolytic and dependent on amino/organic acids to fuel metabolism. Additionally, gastric species lack de novo biosynthetic pathways for several amino acids and purines found in EHS and instead rely on environmental uptake/salvage pathways. Comparison of virulence factor genes between gastric and EHS genomes identified overlapping yet distinct profiles and included canonical cytotoxins, outer membrane proteins, secretion systems, and survival factors. Conclusions The major differences in predicted metabolic function suggest gastric species and EHS may have evolved for survival in the nutrient-rich stomach versus the nutrient-devoid environments, respectively. Contrasting virulence factor gene profiles indicate gastric species and EHS may utilize different pathogenic mechanisms to chronically infect hosts and cause inflammation and tissue damage. The findings from this study provide new insights into the genetic differences underlying gastric versus EHS and support the need for future experimental studies to characterize these pathogens.