Ten years of pan-genome analyses

Comparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.

Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus

Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.

Globin phylogeny, evolution and function, the newest update

Our globin census update allows us to refine our vision of globin origin, evolution, and structure to function relationship in the context of the currently accepted tree of life. The modern globin domain originates as a single domain, three-over-three α-helical folded structure before the diversification of the kingdoms of life (Bacteria, Archaea, Eukarya). Together with the diversification of prokaryotes, three monophyletic globin families (M, S, and T) emerged, most likely in Proteobacteria and Actinobacteria, displaying specific sequence and structural features, and spread by vertical and horizontal gene transfer, most probably already present in the last universal common ancestor (LUCA). Non-globin domains were added, and eventually lost again, creating multi-domain structures in key branches of M- (FHb and Adgb) and the vast majority of S globins, which with their coevolved multi-domain architectures, have predominantly "sensor" functions. Single domain T-family globins diverged into four major groups and most likely display functions related to reactive nitrogen and oxygen species (RNOS) chemistry, as well as oxygen storage/transport which drives the evolution of its major branches with their characteristic key distal residues (B10, E11, E7, and G8). M-family evolution also lead to distinctive major types (FHb and Fgb, Ngb, Adgb, GbX vertebrate Gbs), and shows the shift from high oxygen affinity controlled by TyrB10-Gln/AsnE11 likely related to RNOS chemistry in microorganisms, to a moderate oxygen affinity storage/transport function controlled by hydrophobic B10/E11-HisE7 in multicellular animals.

Leaf morphology related genes revealed by integrating Pan-transcriptome, GWAS and eQTL analyses in a Liriodendron population

Leaf plays an indispensable role in plant development and growth. Although many known genes related to leaf morphology development have been identified, elucidating the complex genetic basis of leaf morphological traits remains a challenge. Liriodendron plants are common ornamental trees due to their unique leaf shapes, while the molecular mechanism underlying Liriodendron leaf morphogenesis has remained unknown. Herein, we firstly constructed a population-level pan-transcriptome of Liriodendron from 81 accessions to explore the expression presence or absence variations (ePAVs), global expression differences at the population level, as well as differentially expressed genes (DEGs) between the Liriodendron chinense and Liriodendron tulipifera accessions. Subsequently, we integrated a genome-wide association study (GWAS), expression quantitative trait loci (eQTL), and transcriptome-wide association study (TWAS) to identify candidate genes related to leaf morphology. Through GWAS analysis, we identified 18 and 17 significant allelic loci in the leaf size and leaf shape modules, respectively. In addition, we discerned 16 candidate genes in relation to leaf morphological traits via TWAS. Further, integrating the co-localization results of GWAS and eQTL, we determined two regulatory hotspot regions, hot88 and hot758, related to leaf size and leaf shape, respectively. Finally, co-expression analysis, eQTL, and linkage mapping together demonstrated that Lchi_4g10795 regulate their own expression levels through cis-eQTL to affect the expression of downstream genes and cooperatively participate in the development of Liriodendron leaf morphology. These findings will improve our understanding of the molecular regulatory mechanism of Liriodendron leaf morphogenesis and will also accelerate molecular breeding of Liriodendron.

The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.

The contours of evolution: In defence of Darwin's tree of life paradigm

Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.

Genotypic Profiling, Functional Analysis, Cholesterol-Lowering Ability, and Angiotensin I-Converting Enzyme (ACE) Inhibitory Activity of Probiotic Lactiplantibacillus plantarum K25 via Different Approaches

Due to its alleged health advantages, several uses in biotechnology and food safety, the well-known probiotic strain Lactiplantibacillus plantarum K25 has drawn interest. This in-depth investigation explores the genetic diversity, makeup, and security characteristics of the microbial genome of L. plantarum K25, providing insightful knowledge about its genotypic profile and functional characteristics. Utilizing cutting-edge bioinformatics techniques like comparative genomics, pan-genomics, and genotypic profiling was carried out to reveal the strain's multidimensional potential in various fields. The results not only add to our understanding of the genetic makeup of L. plantarum K25 but also show off its acceptability in various fields, notably in biotechnology and food safety. The explanation of evolutionary links, which highlights L. plantarum K25's aptitude as a probiotic, is one notable finding from this research. Its safety profile, which is emphasized by the absence of genes linked to antibiotic resistance, is crucial and supports its status as a promising probiotic option.

Deciphering the gastrointestinal carriage of Klebsiella pneumoniae

Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.

A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes

High-throughput sequencing-based methods for bulked segregant analysis (BSA) allow for the rapid identification of genetic markers associated with traits of interest. BSA studies have successfully identified qualitative (binary) and quantitative trait loci (QTLs) using QTL mapping. However, most require population structures that fit the models available and a reference genome. Instead, high-throughput short-read sequencing can be combined with BSA of k-mers (BSA-k-mer) to map traits that appear refractory to standard approaches. This method can be applied to any organism and is particularly useful for species with genomes diverged from the closest sequenced genome. It is also instrumental when dealing with highly heterozygous and potentially polyploid genomes without phased haplotype assemblies and for which a single haplotype can control a trait. Finally, it is flexible in terms of population structure. Here, we apply the BSA-k-mer method for the rapid identification of candidate regions related to seed spot and seed size in diploid potato. Using a mixture of F1 and F2 individuals from a cross between 2 highly heterozygous parents, candidate sequences were identified for each trait using the BSA-k-mer approach. Using parental reads, we were able to determine the parental origin of the loci. Finally, we mapped the identified k-mers to a closely related potato genome to validate the method and determine the genomic loci underlying these sequences. The location identified for the seed spot matches with previously identified loci associated with pigmentation in potato. The loci associated with seed size are novel. Both loci are relevant in future breeding toward true seeds in potato.

Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere

BACKGROUND

Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

RESULTS

Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

CONCLUSIONS

The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.

Pan-Genome Plasticity and Virulence Factors: A Natural Treasure Trove for Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative pathogen responsible for a variety of community- and hospital-acquired infections. It is recognized as a life-threatening pathogen among hospitalized individuals and, in particular, immunocompromised patients in many countries. A. baumannii, as a member of the ESKAPE group, encompasses high genomic plasticity and simultaneously is predisposed to receive and exchange the mobile genetic elements (MGEs) through horizontal genetic transfer (HGT). Indeed, A. baumannii is a treasure trove that contains a high number of virulence factors. In accordance with these unique pathogenic characteristics of A. baumannii, the authors aim to discuss the natural treasure trove of pan-genome and virulence factors pertaining to this bacterial monster and try to highlight the reasons why this bacterium is a great concern in the global public health system.

Diversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures

We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.

Whole-genome sequencing of extensively drug-resistant Salmonella enterica serovar Typhi clinical isolates from the Peshawar region of Pakistan

BACKGROUND

Typhoid fever, caused by Salmonella enterica serovar Typhi, is a significant public health concern due to the escalating of antimicrobial resistance (AMR), with limited treatment options for extensively drug-resistant (XDR) S. Typhi strains pose a serious threat to disease management and control. This study aimed to investigate the genomic characteristics, epidemiology and AMR genes of XDR S. Typhi strains from typhoid fever patients in Pakistan.

METHODOLOGY

We assessed 200 patients with enteric fever symptoms, confirming 65 S. Typhi cases through culturing and biochemical tests. Subsequent antimicrobial susceptibility testing revealed 40 cases of extensively drug-resistant (XDR) and 25 cases of multi-drug resistance (MDR). Thirteen XDR strains were selected for whole-genome sequencing, to analyze their sequence type, phylogenetics, resistance genes, pathogenicity islands, and plasmid sequences using variety of data analysis resources. Pangenome analysis was conducted for 140 XDR strains, including thirteen in-house and 127 strains reported from other regions of Pakistan, to assess their genetic diversity and functional annotation.

RESULTS

MLST analysis classified all isolates as sequence type 1 (ST-1) with 4.3.1.1. P1 genotype characterization. Prophage and Salmonella Pathogenicity Island (SPI) analysis identified intact prophages and eight SPIs involved in Salmonella's invasion and replication within host cells. Genome data analysis revealed numerous AMR genes including dfrA7, sul1, qnrS1, TEM-1, Cat1, and CTX-M-15, and SNPs associated with antibiotics resistance. IncY, IncQ1, pMAC, and pAbTS2 plasmids, conferring antimicrobial resistance, were detected in a few XDR S. Typhi strains. Phylogenetic analysis inferred a close epidemiological linkage among XDR strains from different regions of Pakistan. Pangenome was noted closed among these strains and functional annotation highlighted genes related to metabolism and pathogenesis.

CONCLUSION

This study revealed a uniform genotypic background among XDR S. Typhi strains in Pakistan, signifying a persistence transmission of a single, highly antibiotic-resistant clone. The closed pan-genome observed underscores limited genetic diversity and highlights the importance of genomic surveillance for combating drug-resistant typhoid infections.

Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens

The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome

Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.

High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis

The human-pathogenic Enterobacter species are widely distributed in diverse environmental conditions, however, the understanding of the virulence factors and genetic variations within the genus is very limited. In this study, we performed comparative genomics analysis of 49 strains originated from diverse niches and belonged to eight Enterobacter species, in order to further understand the mechanism of adaption to the environment in Enterobacter. The results showed that they had an open pan-genome and high genomic diversity which allowed adaptation to distinctive ecological niches. We found the number of secretion systems was the highest among various virulence factors in these Enterobacter strains. Three types of T6SS gene clusters including T6SS-A, T6SS-B and T6SS-C were detected in most Enterobacter strains. T6SS-A and T6SS-B shared 13 specific core genes, but they had different gene structures, suggesting they probably have different biological functions. Notably, T6SS-C was restricted to E. cancerogenus. We detected a T6SS gene cluster, highly similar to T6SS-C (91.2%), in the remote related Citrobacter rodenitum, suggesting that this unique gene cluster was probably acquired by horizontal gene transfer. The genomes of Enterobacter strains possess high genetic diversity, limited number of conserved core genes, and multiple copies of T6SS gene clusters with differentiated structures, suggesting that the origins of T6SS were not by duplication instead by independent acquisition. These findings provide valuable information for better understanding of the functional features of Enterobacter species and their evolutionary relationships.

pyPGCF: A Python Software for Phylogenomic Analysis, Species Demarcation, Identification of Core, and Fingerprint Proteins of Bacterial Genomes That Are Important for Plants

This computational protocol describes how to use pyPGCF, a python software package that runs in the linux environment, in order to analyze bacterial genomes and perform: (i) phylogenomic analysis, (ii) species demarcation, (iii) identification of the core proteins of a bacterial genus and its individual species, (iv) identification of species-specific fingerprint proteins that are found in all strains of a species and, at the same time, are absent from all other species of the genus, (v) functional annotation of the core and fingerprint proteins with eggNOG, and (vi) identification of secondary metabolite biosynthetic gene clusters (smBGCs) with antiSMASH. This software has already been implemented to analyze bacterial genera and species that are important for plants (e.g., Pseudomonas, Bacillus, Streptomyces). In addition, we provide a test dataset and example commands showing how to analyze 165 genomes from 55 species of the genus Bacillus. The main advantages of pyPGCF are that: (i) it uses adjustable orthology cut-offs, (ii) it identifies species-specific fingerprints, and (iii) its computational cost scales linearly with the number of genomes being analyzed. Therefore, pyPGCF is able to deal with a very large number of bacterial genomes, in reasonable timescales, using widely available levels of computing power.

Pan-Genomic Analysis Identifies the Chinese Strain as a New Subspecies of Xanthomonas fragariae

Xanthomonas fragariae is classified as a quarantine pathogen by the European and Mediterranean Plant Protection Organization. It commonly induces typical angular leaf spot (ALS) symptoms in strawberry leaves. X. fragariae strains from China (YL19, SHAQP01, and YLX21) exhibit ALS symptoms in leaves and more severe symptoms of dry cavity rot in strawberry crowns. Conversely, strains from other countries do not cause severe dry cavity rot symptoms in strawberries. After employing multilocus sequence analysis (MLSA), average nucleotide identity (ANI), and amino acid identity (AAI), we determined that Chinese strains of X. fragariae are genetically distinct from other strains and can be considered a new subspecies. Subsequent analysis of 63 X. fragariae genomes published at NCBI using IPGA and EDGAR3.0 revealed the pan-genomic profile, with 1,680 shared genes present in all 63 strains, including 71 virulence-related genes. Additionally, we identified 123 genes exclusive to all the Chinese strains, encompassing 12 virulence-related genes. The qRT-PCR analysis demonstrated that the expression of XopD, XopG1, CE8, GT2, and GH121 out of 12 virulence-related genes of Chinese strains (YL19) exhibited a constant increase in the early stages (6, 24, 54, and 96 hours postinoculation [hpi]) of strawberry leaf infected by YL19. So, the presence of XopD, XopG1, CE8, GT2, and GH121 in Chinese strains may play important roles in the early infection process of Chinese strains. These findings offer novel insights into comprehending the population structure and variation in the pathogenic capacity of X. fragariae.

Pangenome diversification and resistance gene characterization in Salmonella Typhi prioritized RfaJ as a significant therapeutic marker

BACKGROUND

Salmonella Typhi stands as the etiological agent responsible for the onset of human typhoid fever. The pressing demand for innovative therapeutic targets against S. Typhi is underscored by the escalating prevalence of this pathogen and the severe nature of its infections. Consequently, this study employs pangenome analysis to scrutinize 119 S. Typhi-resistant strains, aiming to identify the most promising therapeutic targets originating from its core genome.

RESULTS

Subtractive genomics was employed to systematically eliminate non-homologous (n=1147), essential (n=551), drug-like (n=80), and pathogenicity-related (n=18) proteins from the initial pool of 3351 core genome proteins. Consequently, lipopolysaccharide 1,2-glucosyltransferase RfaJ was designated as the optimal pharmacological target due to its potential versatility. Furthermore, a compendium of 9000 FDA-approved compounds was repurposed for evaluation against the RfaJ drug target, with the specific intent of prioritizing novel, high-potency therapeutic candidates for combating S. Typhi. Ultimately, four compounds, namely DB00549 (Zafirlukast), DB15637 (Fluzoparib), DB15688 (Zavegepant), and DB12411 (Bemcentinib), were singled out as potential inhibitors based on the ligand-protein binding affinity (indicated by the lowest anticipated binding energy) and the overall stability of these compounds. Notably, molecular dynamics simulations, conducted over a 50 nanosecond interval, convincingly demonstrated the stability of these compounds in the context of the RfaJ protein.

CONCLUSION

In summary, the present findings hold significant promise as an initial stride in the broader drug discovery endeavor against S. Typhi infections. However, the experimental validation of the identified drug target and drug candidate is further required to increase the effectiveness of the applied methodology.

Biosynthetic gene cluster profiling from North Java Sea Virgibacillus salarius reveals hidden potential metabolites

Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia's North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an "open" pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.

Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers

The wide adoption of bacterial genome sequencing and encoding both core and accessory genome variation using k-mers has allowed bacterial genome-wide association studies (GWAS) to identify genetic variants associated with relevant phenotypes such as those linked to infection. Significant limitations still remain because of k-mers being duplicated across gene clusters and as far as the interpretation of association results is concerned, which affects the wider adoption of GWAS methods on microbial data sets. We have developed a simple computational method (panfeed) that explicitly links each k-mer to their gene cluster at base-resolution level, which allows us to avoid biases introduced by a global de Bruijn graph as well as more easily map and annotate associated variants. We tested panfeed on two independent data sets, correctly identifying previously characterized causal variants, which demonstrates the precision of the method, as well as its scalable performance. panfeed is a command line tool written in the python programming language and is available at https://github.com/microbial-pangenomes-lab/panfeed.

CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes

MOTIVATION

Whole genome alignment of eukaryote species remains an important method for the determination of sequence and structural variations and can also be used to ascertain the representative non-redundant core-genome sequence of a population. Many whole genome alignment tools were first developed for the more mature analysis of prokaryote species with few current tools containing the functionality to process larger genomes of eukaryotes as well as genomes of more divergent species. In addition, the functionality of these tools becomes computationally prohibitive due to the significant compute resources needed to handle larger genomes.

RESULTS

In this research, we present CoreDetector, an easy-to-use general-purpose program that can align the core-genome sequences for a range of genome sizes and divergence levels. To illustrate the flexibility of CoreDetector, we conducted alignments of a large set of closely related fungal pathogen and hexaploid wheat cultivar genomes as well as more divergent fly and rodent species genomes. In all cases, compared to existing multiple genome alignment tools, CoreDetector exhibited improved flexibility, efficiency, and competitive accuracy in tested cases.

AVAILABILITY AND IMPLEMENTATION

CoreDetector was developed in the cross platform, and easily deployable, Java language. A packaged pipeline is readily executable in a bash terminal without any external need for Perl or Python environments. Installation, example data, and usage instructions for CoreDetector are freely available from https://github.com/mfruzan/CoreDetector.

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses

BACKGROUND

A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes.

RESULTS

Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables.

CONCLUSIONS

Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.

Recent progress in the genotyping of bovine tuberculosis and its rapid diagnosis via nanoparticle-based electrochemical biosensors

Bovine tuberculosis (bTB) is considered a worldwide infectious zoonotic disease. Mycobacterium bovis causes bTB disease. It is one of the Mycobacterium tuberculosis complex (MTBC) members. MTBC is a clonal complex of close relatives with approximately 99.95% similarity. M. bovis is a spillover pathogen that can transmit from animals to humans and rarely from humans to animals with contact. Genotyping techniques are important to discriminate and differentiate between MTBC species. Spoligotyping and mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) are widely used but they have some limitations. As an alternative, whole genome sequencing approaches have been utilized due to their high-resolution power. They are employed in typing M. bovis and explain the evolutionary and phylogenetic relationships between isolates. The control of bTB disease has attracted a large amount of attention. Rapid and proper diagnosis is necessary for monitoring the disease as an initial step for its control and treatment. Nanotechnology has a potential impact on the rapid diagnosis and treatment of bTB through the use of nanocarrier and metal nanoparticles (NPs). Special attention has been paid to voltammetric and impedimetric electrochemical strategies as facile, sensitive, and selective methods for the efficient detection of tuberculosis. The efficacy of these sensors is enhanced in the presence of NPs, which act as recognition and/or redox probes. Gold, silver, copper, cobalt, graphene, and magnetic NPs, as well as polypyrrole nanowires and multiwalled carbon nanotubes have been employed for detecting tuberculosis. Overall, NP-based electrochemical sensors represent a promising tool for the diagnosis of bTB.

Gene presence/absence variation in Mytilus galloprovincialis and its implications in gene expression and adaptation

Presence/absence variation (PAV) is a well-known phenomenon in prokaryotes that was described for the first time in bivalves in 2020 in Mytilus galloprovincialis. The objective of the present study was to further our understanding of the PAV phenomenon in mussel biology. The distribution of PAV was studied in a mussel chromosome-level genome assembly, revealing a widespread distribution but with hotspots of dispensability. Special attention was given to the effect of PAV in gene expression, since dispensable genes were found to be inherently subject to distortions due to their sparse distribution among individuals. Furthermore, the high expression and strong tissue specificity of some dispensable genes, such as myticins, strongly supported their biological relevance. The significant differences in the repertoire of dispensable genes associated with two geographically distinct populations suggest that PAV is involved in local adaptation. Overall, the PAV phenomenon would provide a key selective advantage at the population level.

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

BACKGROUND

Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches.

RESULTS

EasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson-Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines.

CONCLUSIONS

EasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github ( https://github.com/zdf1987/EasyCGTree4 ).

One Earth: The Equilibrium between the Human and the Bacterial Worlds

Misuse and abuse of antibiotics on humans, cattle, and crops have led to the selection of multi-resistant pathogenic bacteria, the most feared 'superbugs'. Infections caused by superbugs are progressively difficult to treat, with a subsequent increase in lethality: the toll on human lives is predicted to reach 10 million by 2050. Here we review three concepts linked to the growing resistance to antibiotics, namely (i) the Resistome, which refers to the collection of bacterial genes that confer resistance to antibiotics, (ii) the Mobilome, which includes all the mobile genetic elements that participate in the spreading of antibiotic resistance among bacteria by horizontal gene transfer processes, and (iii) the Nichome, which refers to the set of genes that are expressed when bacteria try to colonize new niches. We also discuss the strategies that can be used to tackle bacterial infections and propose an entente cordiale with the bacterial world so that instead of war and destruction of the 'fierce enemy' we can achieve a peaceful coexistence (the One Earth concept) between the human and the bacterial worlds. This, in turn, will contribute to microbial biodiversity, which is crucial in a globally changing climate due to anthropogenic activities.

Species-specific responses of marine bacteria to environmental perturbation

Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.

Characterization of three rapidly growing novel Mycobacterium species with significant polycyclic aromatic hydrocarbon bioremediation potential

Mycobacterium species exhibit high bioremediation potential for the degradation of polycyclic aromatic hydrocarbons (PAHs) that are significant environmental pollutants. In this study, three Gram-positive, rapidly growing strains (YC-RL4T, MB418T, and HX176T) were isolated from petroleum-contaminated soils and were classified as Mycobacterium within the family Mycobacteriaceae. Genomic average nucleotide identity (ANI; < 95%) and digital DNA-DNA hybridization (dDDH; < 70%) values relative to other Mycobacterium spp. indicated that the strains represented novel species. The morphological, physiological, and chemotaxonomic characteristics of the isolates also supported their affiliation with Mycobacterium and their delineation as novel species. The strains were identified as Mycobacterium adipatum sp. nov. (type strain YC-RL4T = CPCC 205684T = CGMCC 1.62027T), Mycobacterium deserti sp. nov. (type strain MB418T = CPCC 205710T = KCTC 49782T), and Mycobacterium hippophais sp. nov. (type strain HX176T = CPCC 205372T = KCTC 49413T). Genes encoding enzymes involved in PAH degradation and metal resistance were present in the genomes of all three strains. Specifically, genes encoding alpha subunits of aromatic ring-hydroxylating dioxygenases were encoded by the genomes. The genes were also identified as core genes in a pangenomic analysis of the three strains along with 70 phylogenetically related mycobacterial strains that were previously classified as Mycolicibacterium. Notably, strain YC-RL4T could not only utilize phthalates as their sole carbon source for growth, but also convert di-(2-ethylhexyl) phthalate into phthalic acid. These results indicated that strains YC-RL4T, MB418T, and HX176T were important resources with significant bioremediation potential in soils contaminated by PAHs and heavy metals.

Genomics in the long-read sequencing era

Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.

Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador

Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.

Dynamics of nucleic acid mobility

Advances in sequencing technologies and bioinformatic analyses are accelerating the quantity and quality of data from all domains of life. This rich resource has the potential to reveal a number of important incidences with respect to possible exchange of nucleic acids. Ancient events have impacted species evolution and adaptation to new ecological niches. However, we still lack a full picture of processes ongoing within and between somatic cells, gametes, and different organisms. We propose that events linked to acceptance of alien nucleic acids grossly could be divided into 2 main routes in plants: one, when plants are exposed to extreme challenges and, the second level, a more everyday or season-related stress incited by biotic or abiotic factors. Here, many events seem to comprise somatic cells. Are the transport and acceptance processes of alien sequences random or are there specific regulatory systems not yet fully understood? Following entrance into a new cell, a number of intracellular processes leading to chromosomal integration and function are required. Modification of nucleic acids and possibly exchange of sequences within a cell may also occur. Such fine-tune events are most likely very common. There are multiple questions that we will discuss concerning different types of vesicles and their roles in nucleic acid transport and possible intracellular sequence exchange between species.

Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.

Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex

BACKGROUND

Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues.

RESULTS

To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness.

CONCLUSIONS

Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.

An antimicrobial thiopeptide producing novel actinomycetes Streptomyces terrae sp. nov., isolated from subsurface soil of arable land

An antimicrobial producing Gram-positive, aerobic, nonmotile, and filamentous actinobacterial strain SKN60T was isolated from soil The isolate exhibited 99.3% and 99.0% identity with Streptomyces laurentii ATCC 31255T and S. roseicoloratus TRM 44457T, respectively, in 16S rRNA gene sequence analysis. However, the genome sequence displayed maximum ANI (88.45%) and AAI (85.61%) with S. roseicoloratus TRM 44457T. Similarly, the dDDH showed 33.7% identity with S. roseicoloratus TRM 44457T. It formed a cluster with S. roseicoloratus TRM 44457T and S. laurentii ATCC 31255T in phylogenomic tree. Cell wall analysis revealed the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine as major polar lipids and diaminopimelic acid as diagnostic diamino acid. Major fatty acids were iso-C15:0, anteiso-C15:0, and iso-C16:0. The G+C content was found to be 72.3 mol%. Genome sequence analysis using antiSMASH database showed occurrence of a thiopeptide biosynthesis gene cluster with 94% similarity to berninamycin from S. bernensis UC5144. The mass of 1146 Da is identical with berninamycin. But subtle differences observed in leader peptide sequence of thiopeptide and berninamycin. Notably, S. bernensis is not validly reported and thus SKN60T is the only strain containing berninamycin BGC as no other phylogenetic relative had it. Additionally, strain SKN60T differed in phenotypic and genetic characteristics with all phylogenetic relatives of the genus Streptomyces. Therefore, it is proposed as a novel species with the name Streptomyces terrae sp. nov. strain SKN60T (=MTCC 13163T; = JCM 35768T).

Pangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads

Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.

Ideotype breeding and genome engineering for legume crop improvement

Ideotype breeding is a strategy whereby traits are modeled a priori and then introduced into a model or crop species to assess their impact on yield. Thus, knowledge about the connection between genotype and phenotype is required for ideotype breeding to be deployed successfully. The growing understanding of the genetic basis of yield-related traits, combined with increasingly efficient genome engineering tools, improved transformation efficiency, and high-throughput genotyping of regenerants paves the way for the widespread adoption of ideotype breeding as a complement to conventional breeding. We briefly discuss how ideotype breeding, coupled with such state-of-the-art biotechnological tools, could contribute to knowledge-based legume breeding and accelerate yield gains to ensure food security in the coming decades.

Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman

Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H₂ and CH₄. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO₂, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.

Site-specialization of human oral Gemella species

Gemella species are core members of the human oral microbiome in healthy subjects and are regarded as commensals, although they can cause opportunistic infections. Our objective was to evaluate the site-specialization of Gemella species among various habitats within the mouth by combining pangenomics and metagenomics. With pangenomics, we identified genome relationships and categorized genes as core and accessory to each species. With metagenomics, we identified the primary oral habitat of individual genomes. Our results establish that the genomes of three species, G. haemolysans, G. sanguinis and G. morbillorum, are abundant and prevalent in human mouths at different oral sites: G. haemolysans on buccal mucosa and keratinized gingiva; G. sanguinis on tongue dorsum, throat, and tonsils; and G. morbillorum in dental plaque. The gene-level basis of site-specificity was investigated by identifying genes that were core to Gemella genomes at a specific oral site but absent from other Gemella genomes. The riboflavin biosynthesis pathway was present in G. haemolysans genomes associated with buccal mucosa but absent from the rest of the genomes. Overall, metapangenomics show that Gemella species have clear ecological preferences in the oral cavity of healthy humans and provides an approach to identifying gene-level drivers of site specificity.

In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1

A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO₄ (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.

A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future, pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this review, we mainly discuss how pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis

BACKGROUND

The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance.

METHODS

A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.

RESULTS

The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the bla_OXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621.

CONCLUSIONS

Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.

Validation of a male-specific DNA marker confirms XX/XY-type sex determination in several Hungarian strains of African catfish (Clarias gariepinus)

African catfish (Clarias gariepinus) is a promising food fish species with significant potential and growing mass of production in freshwater aquaculture. Male African catfish possess improved production characteristics over females, therefore the use of monosex populations could be advantageous for aquaculture production. However, our knowledge about the sex determination mechanism of this species is still limited and controversial. A previously isolated male-specific DNA marker (CgaY1) was validated using offspring groups from targeted crosses (n = 630) and it was found to predict the sex of 608 individuals correctly (96.43% accuracy). Using the proportion of recombinants, we estimated the average genetic distance between the potential sex determination locus and the sex-specific marker to be 3.57 cM. As an earlier study suggested that both XX/XY and ZZ/ZW systems coexist in this species, we tested the applicability of their putative 'moderately sex-linked loci' and found that no sex-specific amplification could be detected for any of them. In addition, temperature-induced masculinization suggested by others was also tested, but no such effect was detected in our stocks when the published parameters were used for heat treatment. Altogether, our results support an exclusive XX/XY sex determination system in our African catfish stock and indicate a good potential for the future use of this male-specific DNA marker in research and commercial production.

Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System

During the last century enormous progress has been made in the understanding of biological diversity, involving a dramatic shift from macroscopic to microscopic organisms. The question now arises as to whether the Natural System introduced by Carl Linnaeus, which has served as the central system for organizing biological diversity, can accommodate the great expansion of diversity that has been discovered. Important discoveries regarding biological diversity have not been fully integrated into a formal, coherent taxonomic system. In addition, because of taxonomic challenges and conflicts, various proposals have been made to abandon key aspects of the Linnaean system. We review the current status of taxonomy of the living world, focussing on groups at the taxonomic level of phylum and above. We summarize the main arguments against and in favour of abandoning aspects of the Linnaean system. Based on these considerations, we conclude that retaining the Linnaean Natural System provides important advantages. We propose a relatively small number of amendments for extending this system, particularly to include the named rank of world (Latin alternative mundis) formally to include non-cellular entities (viruses), and the named rank of empire (Latin alternative imperium) to accommodate the depth of diversity in (unicellular) eukaryotes that has been uncovered. We argue that in the case of both the eukaryotic domain and the viruses the cladistic approach intrinsically fails. However, the resulting semi-cladistic system provides a productive way forward that can help resolve taxonomic challenges. The amendments proposed allow us to: (i) retain named taxonomic levels and the three-domain system, (ii) improve understanding of the main eukaryotic lineages, and (iii) incorporate viruses into the Natural System. Of note, the proposal described herein is intended to serve as the starting point for a broad scientific discussion regarding the modernization of the Linnaean system.

Antimony oxidation and whole genome sequencing of Phytobacter sp. X4 isolated from contaminated soil near a flotation site

The conversion of the more toxic Sb(III) into less toxic Sb(V) is an effective strategy for the treatment of antimony-contaminated sites. In this study, a strain, Phytobacter sp. X4, which can tolerate high concentrations of antimony and can use nitrate as an electron acceptor for Sb(III) oxidation under anaerobic conditions, was isolated from the deep soil of an antimony mine flotation tailing. Unlike other antimony oxidizing bacteria, X4 oxidized better under high Sb(III) concentration, and the oxidation efficiency of 10 mM Sb(III) reached the maximum at 110 h with 61.8 %. Kinetic study showed X4 yielded a V_max of 1.093 μM∙min^-1 and a K_m of 718.2 μM. The genome of Phytobacter sp. X4 consists of a complete circular chromosome and two plasmids. In addition, X4 had more metal(loid)s resistance genes and highly expressed genes than other Phytobacter spp., reflecting its stronger adaptive advantage in harsh survival environments. We also analyzed the origin and evolution of arsB, arsC, and arsH, which may have been transferred horizontally from other species. iscR and arsH may have an important contribution to Sb(III) oxidation. Thus, Phytobacter sp. X4 has a good ability to remediate high antimony-contaminated sites and can be applied to an anaerobic environment.

Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments

Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.

Long non-coding RNAs reveal new regulatory mechanisms controlling gene expression

A plethora of non-coding RNAs have been found in eukaryotes, notably with the advent of modern sequencing technologies to analyze the transcriptome. Apart from the well-known housekeeping RNA genes (such as the ribosomal RNA or the transfer RNA), many thousands of transcripts detected are not evidently linked to a protein-coding gene. These, so called non-coding RNAs, may code for crucial regulators of gene expression, the small si/miRNAs, for small peptides (translated under specific conditions) or may act as long RNA molecules (antisense, intronic or intergenic long non-coding RNAs or lncRNAs). The lncRNAs interact with members of multiple machineries involved in gene regulation. In this review, we discussed about how plant lncRNAs permitted to discover new regulatory mechanisms acting in epigenetic control, chromatin 3D structure and alternative splicing. These novel regulations diversified the expression patterns and protein variants of target protein-coding genes and are an important element of the response of plants to environmental stresses and their adaptation to changing conditions.

Site Specialization of Human Oral Veillonella Species

Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.

Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication

Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.