The Pathogen-Host Interactions database (PHI-base): additions and future developments

Building resource-efficient community databases using open-source software

The unprecedented volume of big data being routinely generated for nonmodel crop species, coupled with advanced technology enabling the use of big data in breeding, gives further impetus for the need to have access to crop community databases, where all relevant data are curated and integrated. Funding for such databases is, however, insufficient and intermittent, resulting in the data being underutilized. While increased awareness of the importance of funding databases is important, it is practically necessary to find a more efficient way to build a community database. To meet the need for integrated database resources for various crop genomics, genetics, and breeding research communities, we have built five crop databases over the last decade using an open-source database platform and software. We describe the system and methods used for database construction, curation, and analysis protocols, and the data and tools that are available in these five crop databases. Database URL: The Genome Database for Rosaceae (GDR, www.rosaceae.org), the Genome Database for Vaccinium (GDV, www.vaccinium.org), the Citrus Genome Database (CGD, www.citrusgenomedb.org), the Pulse Crop Database (PCD, www.pulsedb.org), and CottonGen (www.cottongen.org).

PHI-base - the multi-species pathogen-host interaction database in 2025

The Pathogen-Host Interactions Database (PHI-base) has, since 2005, provided manually curated genes from fungal, bacterial and protist pathogens that have been experimentally verified to have important pathogenicity, virulence and/or effector functions during different types of interactions involving human, animal, plant, invertebrate and fungal hosts. PHI-base provides phenotypic annotation and genotypic information for both native and model host interactions, including gene alterations that do not alter the phenotype of the interaction. In this article, we describe major updates to PHI-base. The latest version of PHI-base, 4.17, contains a 19% increase in genes and a 23% increase in interactions relative to version 4.12 (released September 2022). We also describe the unification of data in PHI-base 4 with the data curated from a new curation workflow (PHI-Canto), which forms the first complete release of PHI-base version 5.0. Additionally, we describe adding support for the Frictionless Data framework to PHI-base 4 datasets, new ways of sharing interaction data with the Ensembl database, an analysis of the conserved orthologous genes in PHI-base, and the increasing variety of research studies that make use of PHI-base. PHI-base version 4.17 is freely available at www.phi-base.org and PHI-base version 5.0 is freely available at phi5.phi-base.org.

Characterization of a Bacterium Isolated from Hydrolyzed Instant Sea Cucumber Apostichopus japonicus Using Whole-Genome Sequencing and Metabolomics

Autolysis in the sea cucumber Apostichopus japonicus is typically triggered by degradation caused by microorganisms within their bodies. However, information on this topic remains limited. Recently, we isolated and purified a bacterial strain from hydrolyzed instant sea cucumber samples. To investigate its potential role in the autolysis process, this study employed whole-genome sequencing and metabolomics to explore its genetic and metabolic characteristics. The identified strain was classified as Lysinibacillus xylanilyticus and designated with the number XL-2024. Its genome size is 5,075,210 bp with a GC content of 37.33%, encoding 5275 genes. Functional database comparisons revealed that the protein-coding genes were distributed among glucose metabolism hydrolase, metal hydrolase, lysozyme, cell wall hydrolase, and CAZymes. Compared to 20 closely related strains, L. xylanilyticus XL-2024 shared 1502 core homologous genes and had 707 specific genes. These specific genes were mainly involved in the carbohydrate metabolism pathway and exhibited glycosyl bond hydrolase activity. Metabolomic analysis showed that L. xlanilyticus XL-2024 produced several metabolites related to polysaccharide degradation, including peptidase, glucanase, and pectinase. Additionally, the presence of antibacterial metabolites such as propionic acid and ginkgo acid among its metabolites may enhance the stability of the sea cucumber hydrolysate. In summary, L. xylanilyticus XL-2024 may play a pivotal role in the autolysis of A. japonicus. The results of this study provide a strong foundation for understanding how to prevent autolysis in A. japonicus and for better utilizing L. xylanilyticus XL-2024.

Whole-Genome sequencing of Calonectria dianii: An important pathogen causing Eucalyptus leaf blight

Eucalyptus leaf blight, caused by Calonectria spp., significantly impacts the global Eucalyptus industry. Calonectria dianii, as one of the predominant causal agents, poses a serious threat to Eucalyptus plantations in China. To enhance our understanding of its pathogenic mechanisms, we sequenced the genome of C. dianii RIFT 6520 using both Nanopore PromethION and Illumina NovaSeq PE150 platforms. Our analysis revealed a 61.76 Mb genome comprising 30 contigs with an N50 of 4,726,631 bp, a GC content of 49.74 %, and 10,184 predicted coding genes. Additionally, comparative genomic analysis between C. dianii and seven other significant plant-pathogenic Calonectria species was conducted. This analysis provided insights into the evolutionary relationships and adaptive mechanisms of these pathogens. Our study elucidates the genetic basis of C. dianii's pathogenicity and evolution, providing valuable information for future research on its molecular interactions with Eucalyptus and aiding in the development of precise control measures for Eucalyptus leaf blight.

Succeed to culture a novel lineage symbiotic bacterium of Mollicutes which widely found in arthropods intestine uncovers the potential double-edged sword ecological function

Symbiotic gut bacteria play crucial role in host health. Symbionts are widely distributed in arthropod intestines, but their ecological functions are poorly understood due to the inability to cultivate them. Members of Candidatus Bacilliplasma (CB) are widely distributed in crustacean intestine and maybe commensals with hosts, but the paucity of pure cultures has limited further insights into their physiologies and functions. Here, four strains of representative CB bacteria in shrimp intestine were successfully isolated and identified as members of a novel Order in the Phylum Mycoplasmatota. Through genome assembly, the circular genome maps of the four strains were obtained, and the number of coding genes ranged from 1,886 to 1,980. Genomic analysis suggested that the bacteria were missing genes for many critical pathways including the TCA cycle and biosynthesis pathways for amino acids and coenzyme factors. The analysis of 16S amplification data showed that Shewanella, Pseudomonas and CB were the dominant at the genera level in the intestine of Penaeus vannamei. Ecological functional experiments revealed that the strains were symbionts and colonized shrimp intestines. Our valued findings can greatly enhance our understanding and provides new insights into the potentially significant role of uncultured symbiotic bacteria in modulating host health.

Screening of promising molecules against potential drug targets in Yersinia pestis by integrative pan and subtractive genomics, docking and simulation approach

This study focuses on Yersinia pestis, the bacterium responsible for plague, which posed a severe threat to public health in history. Despite the availability of antibiotics treatment, the emergence of antibiotic resistance in this pathogen has increased challenges of controlling the infections and plague outbreaks. The development of new drug targets and therapies is urgently needed. This research aims to identify novel protein targets from 28 Y. pestis strains by the integrative pan-genomic and subtractive genomics approach. Additionally, it seeks to screen out potential safe and effective alternative therapies against these targets via high-throughput virtual screening. Targets should lack homology to human, gut microbiota, and known human 'anti-targets', while should exhibit essentiality for pathogen's survival and virulence, druggability, antibiotic resistance, and broad spectrum across multiple pathogenic bacteria. We identified two promising targets: the aminotransferase class I/class II domain-containing protein and 3-oxoacyl-[acyl-carrier-protein] synthase 2. These proteins were modeled using AlphaFold2, validated through several structural analyses, and were subjected to molecular docking and ADMET analysis. Molecular dynamics simulations determined the stability of the ligand-target complexes, providing potential therapeutic options against Y. pestis.

Annotation of Functions of Sequences of Concern and Its Relevance to the New Biosecurity Regulatory Framework in the United States

Introduction

Recent regulations from United States Government agencies reshape the screening of synthetic nucleic acids. These take a step away from categorizing hazard on the basis of "bad" taxa and invoke the function of the sequence in pathogenesis or intoxication. Ascertaining functions related to pathogenesis and distinguishing these from other molecular abilities that are unproblematic is not simple. Some have suggested that this information can be readily obtained from existing databases of pathogens.

Objectives

We evaluate how virulence factors are described in current databases of pathogens and their adequacy for biothreat data science. We discuss limitations of how virulence factors have been conceived and propose using the sequence of concern (SoC) term to distinguish sequences with biothreat from those without. We discuss ways in which databases of SoCs might be implemented for research and regulatory purposes. We describe ongoing work improving functional descriptions of SoCs.

Methods

We assess the adequacy of descriptions of virulence factors in pathogen databases following extensive engagement with the literature in microbial pathogenesis.

Results/Conclusions

Descriptions of virulence factors in pathogen databases are inadequate for understanding biothreats. Many are not biothreats and would not be concerning if transferred to another pathogen. New gene ontology terms have been authored, and those specific to pathogenic viral processes are being generalized to make them relevant to other pathogenic taxa. This allows better understanding by humans and better recognition by machines. A database of annotated functions of SoCs could benefit the evolving biosecurity regulatory framework in the United States.

New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes

Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic Fusarium lateritium (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic Fusarium oxysporum Fo4287 and endophytic Fusarium oxysporum Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic F. lateritium has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical Fusarium spp. toxins, and a lack of the key Fusarium spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants.

Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb

'Candidatus Phytoplasma' genus, a group of fastidious phloem-restricted bacteria, can infect a wide variety of both ornamental and agro-economically important plants. Phytoplasmas secrete effector proteins responsible for the symptoms associated with the disease. Identifying and characterizing these proteins is of prime importance for expanding our knowledge of the molecular bases of the disease. We faced the challenge of identifying phytoplasma's effectors by developing LEAPH, a machine learning ensemble predictor composed of four models. LEAPH was trained on 479 proteins from 53 phytoplasma species, described by 30 features. LEAPH achieved 97.49% accuracy, 95.26% precision and 98.37% recall, ensuring a low false-positive rate and outperforming available state-of-the-art methods. The application of LEAPH to 13 phytoplasma proteomes yields a comprehensive landscape of 2089 putative pathogenicity proteins. We identified three classes according to different secretion models: 'classical', 'classical-like' and 'non-classical'. Importantly, LEAPH identified 15 out of 17 known experimentally validated effectors belonging to the three classes. Furthermore, to help the selection of novel candidates for biological validation, we applied the Self-Organizing Maps algorithm and developed a Shiny app called EffectorComb. LEAPH and the EffectorComb app can be used to boost the characterization of putative effectors at both computational and experimental levels, and can be employed in other phytopathological models.

Evolution and related pathogenic genes of Pseudodiploöspora longispora on Morchella based on genomic characterization and comparative genomic analysis

True morels (Morchella) are globally renowned medicinal and edible mushrooms. White mold disease caused by fungi is the main disease of Morchella, which has the characteristics of wide incidence and strong destructiveness. The disparities observed in the isolation rates of different pathogens indicate their varying degrees of host adaptability and competitive survival abilities. In order to elucidate its potential mechanism, this study, the pathogen of white mold disease from Dafang county, Guizhou Province was isolated and purified, identified as Pseudodiploöspora longispora by morphological, molecular biological and pathogenicity tests. Furthermore, high-quality genome of P. longisporus (40.846 Mb) was assembled N50 of 3.09 Mb, predicts 7381 protein-coding genes. Phylogenetic analysis of single-copy homologous genes showed that P. longispora and Zelopaecilomyces penicillatus have the closest evolutionary relationship, diverging into two branches approximately 50 (44.3-61.4) MYA. Additionally, compared with the other two pathogens causing Morchella disease, Z. penicillatus and Cladobotryum protrusum, it was found that they had similar proportions of carbohydrate enzyme types and encoded abundant cell wall degrading enzymes, such as chitinase and glucanase, indicating their important role in disease development. Moreover, the secondary metabolite gene clusters of P. longispora and Z. penicillatus show a high degree of similarity to leucinostatin A and leucinostatin B (peptaibols). Furthermore, a gene cluster with synthetic toxic substance Ochratoxin A was also identified in P. longispora and C. protrusum, indicating that they may pose a potential threat to food safety. This study provides valuable insights into the genome of P. longispora, contributing to pathogenicity research.

Genome and transcriptome based comparative analysis of Tilletia indica to decipher the causal genes for pathogenicity of Karnal bunt in wheat

Tilletia indica Mitra causes Karnal bunt (KB) in wheat by pathogenic dikaryophase. The present study is the first to provide the draft genomes of the dikaryon (PSWKBGD-3) and its two monosporidial lines (PSWKBGH-1 and 2) using Illumina and PacBio reads, their annotation and the comparative analyses among the three genomes by extracting polymorphic SSR markers. The trancriptome from infected wheat grains of the susceptible wheat cultivar WL711 at 24 h, 48h, and 7d after inoculation of PSWKBGH-1, 2 and PSWKBGD-3 were also isolated. Further, two transcriptome analyses were performed utilizing T. indica transcriptome to extract dikaryon genes responsible for pathogenesis, and wheat transcriptome to extract wheat genes affected by dikaryon involved in plant-pathogen interaction during progression of KB in wheat. A total of 54, 529, and 87 genes at 24hai, 48hai, and 7dai, respectively were upregulated in dikaryon stage while 21, 35, and 134 genes of T. indica at 24hai, 48hai, and 7dai, respectively, were activated only in dikaryon stage. While, a total of 23, 17, and 52 wheat genes at 24hai, 48hai, and 7dai, respectively were upregulated due to the presence of dikaryon stage only. The results obtained during this study have been compiled in a web resource called TiGeR ( http://backlin.cabgrid.res.in/tiger/ ), which is the first genomic resource for T. indica cataloguing genes, genomic and polymorphic SSRs of the three T. indica lines, wheat and T. indica DEGs as well as wheat genes affected by T. indica dikaryon along with the pathogenecity related proteins of T. indica dikaryon during incidence of KB at different time points. The present study would be helpful to understand the role of dikaryon in plant-pathogen interaction during progression of KB, which would be helpful to manage KB in wheat, and to develop KB-resistant wheat varieties.

Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER

Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Identifying and characterizing pathogens effectors is crucial towards their improved control. Because of their poor sequence conservation, effector identification is challenging, and current methods generate too many candidates without indication for prioritizing experimental studies. In most phyla, effectors contain specific sequence motifs which influence their localization and targets in the plant. Therefore, there is an urgent need to develop bioinformatics tools tailored for pathogen effectors. To circumvent these limitations, we have developed MOnSTER a specific tool that identifies clusters of motifs of protein sequences (CLUMPs). MOnSTER can be fed with motifs identified by de novo tools or from databases such as Pfam and InterProScan. The advantage of MOnSTER is the reduction of motif redundancy by clustering them and associating a score. This score encompasses the physicochemical properties of AAs and the motif occurrences. We built up our method to identify discriminant CLUMPs in oomycetes effectors. Consequently, we applied MOnSTER on plant parasitic nematodes and identified six CLUMPs in about 60% of the known nematode candidate parasitism proteins. Furthermore, we found co-occurrences of CLUMPs with protein domains important for invasion and pathogenicity. The potentiality of this tool goes beyond the effector characterization and can be used to easily cluster motifs and calculate the CLUMP-score on any set of protein sequences.

The Development of a Fluorescent Microsatellite Marker Assay for the Pitaya Canker Pathogen (Neoscytalidium dimidiatum)

Pitaya canker, caused by Neoscytalidium dimidiatum, is a destructive disease that significantly threatens the safety of the pitaya industry. The authors of previous studies have mainly focused on its biological characteristics and chemical control. However, there are no molecular markers available thus far that can be used for the population genetics study of this pathogen. In the present study, a draft genome of N. dimidiatum with a total length of 41.46 MB was assembled in which 9863 coding genes were predicted and annotated. In particular, the microsatellite sequences in the draft genome were investigated. To improve the successful screening rate of potentially polymorphic microsatellite makers, another five N. dimidiatum isolates were resequenced and assembled. A total of eight pairs of polymorphic microsatellite primers were screened out based on the polymorphic microsatellite loci after investigating the sequencing and resequencing assemblies of the six isolates. A total of thirteen representative isolates sampled from different pitaya plantations were genotyped in order to validate the polymorphism of the resulting eight markers. The results indicated that these markers were able to distinguish the isolates well. Lastly, a neighbor-joining tree of 35 isolates, sampled from different pitaya plantations located in different regions, was constructed according to the genotypes of the eight molecular markers. The developed tree indicated that these molecular markers had sufficient genotyping capabilities for our test panel of isolates. In summary, we developed a set of polymorphic microsatellite markers in the following study that can effectively genotype and distinguish N. dimidiatum isolates and be utilized in the population genetics study of N. dimidiatum.

Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China

BACKGROUND

Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species.

RESULTS

In this study, we analyzed the morphological, physiological, and genomic characteristics of the newly identified B. porcorum sp. nov. strain QD2021 isolated from pigs. The complete genome sequence of the B. porcorum QD2021 strain consists of a single circular chromosome (2,271,736 bp, 38.51% G + C content), which encodes 2,578 genes. One plasmid with a size of 70,040 bp was detected. A total of 121 scattered repeat sequences, 319 tandem repeat sequences, 4 genomic islands, 5 prophages, 3 CRISPR sequences, and 51 ncRNAs were predicted. The coding genes of the B. porcorum genome were successfully annotated across eight databases (NR, GO, KEGG, COG, TCDB, Pfam, Swiss-Prot and CAZy) and four pathogenicity-related databases (PHI, CARD, VFDB and ARDB). In addition, a comparative genome analysis was performed to explore the evolutionary relationships of B. porcorum QD2021.

CONCLUSIONS

To our knowledge, this is the first study to provide fundamental phenotypic and whole-genome sequences for B. porcorum. Our results extensively expand the current knowledge and could serve as a valuable genomic resource for future research on B. porcorum.

Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics

A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled "shared and unique" proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15-16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew.

Genomic and Proteomic Analyses of Extracellular Products Reveal Major Virulence Factors Likely Accounting for Differences in Pathogenicity to Bivalves between Vibrio mediterranei Strains

Vibrio mediterranei, a bacterial pathogen of bivalves, has exhibited strain-dependent virulence. The mechanisms behind the variations in bivalve pathogenicity between V. mediterranei strains have remained unclear. However, a preliminary analysis of the extracellular product (ECP) proteomes has revealed differences in protein compositions between low- and high-virulence strains; in addition to 1265 shared proteins, 127 proteins have been identified to be specific to one low-virulence strain and 95 proteins to be specific to two high-virulence strains. We further studied the ECP proteins of the three V. mediterranei strains from functional perspectives using integrated genomics and proteomics approaches. The results showed that lipid metabolism, transporter activity and membrane transporter pathways were more enriched in the ECPs of the two high-virulence strains than in those of the low-virulence strain. Additionally, 73 of the 95 high-virulence strain-specific proteins were found to have coding genes in the genome but were not expressed in the low-virulence strain. Moreover, comparisons with known virulence factors in the Virulence Factor Database (VFDB) and the Pathogen-Host Interactions Database (PHI-base) allowed us to predict more than 10 virulence factors in the categories of antimicrobial activity/competitive advantage, the effector delivery system and immune modulation, and the high-virulence strain-specific ECP proteins consisted of a greater percentage of known virulence factors than the low-virulence strain. Particularly, two virulence factors, MtrC and KatG, were identified in the ECPs of the two high-virulence strains but not in those of the low-virulence strain. Most coding genes of the ECP proteins including known virulence factors were identified on chromosome 1 of V. mediterranei. Our findings indicate that variations in virulence factor composition in the bacterial ECPs may partially account for the differences in the bivalve pathogenicity between V. mediterranei strains.

Whole-genome sequencing of Fusarium spp. causing sugarcane root rot on both chewing cane and sugar-making cane

Previously we isolated three Fusarium strains (a F. sacchari strain namely GXUF-1, and another two F. commune strains namely GXUF-2 and GXUF-3), and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila. Considering that Fusarium spp. are a group of widely distributed fungal pathogens, we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar (Guitang42), using a suitable inoculation method established based on infection assays using Badila. We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42, to different extents. To better investigate the potential pathogenicity mechanisms, we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains. The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7-48.2 Mb, with G + C contents of 48.0-48.5%, and 14,154-15,175 coding genes. The coding genes were annotated by multiple public databases, and potential pathogenic genes were predicted using proprietary databases (such as PHI, DFVF, CAZy, etc.). Furthermore, based on evolutionary analysis of the coding sequence, we found that contraction and expansion of gene families occurred in the three Fusarium strains. Overall, our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane, and provide clues to understand the pathogenic mechanisms of Fusarium spp. causing sugarcane root rot.

High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees

OBJECTIVES

Lasiodiplodia pseudotheobromae is an important fungal pathogen associated with die-back, canker and shoot blight in many plant hosts with a wide geographic distribution. The aim of our study was to provide high-quality genome assemblies and sequence annotation resources of L. pseudotheobromae, to facilitate future studies on the systematics, population genetics and genomics of the fungal pathogen L. pseudotheobromae.

DATA DESCRIPTION

High-quality genomes of five L. pseudotheobromae isolates were sequenced based on Oxford Nanopore technology (ONT) and Illumina HiSeq sequencing platform. The total size of each assembly ranged from 43 Mb to 43.86 Mb and over 11,000 protein-coding genes were predicted from each genome. The proteins of predicted genes were annotated using multiple public databases, among the annotated protein-coding genes, more than 4,300 genes were predicted as potential virulence genes by the Pathogen Host Interactions (PHI) database. Moreover, the genome comparative analysis among L. pseudotheobromae and other closely related species revealed that 7,408 gene clusters were shared among them and 152 gene clusters unique to L. pseudotheobromae. This genome and associated datasets provided here will serve as a useful resource for further analyses of this fungal pathogen species.

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.

Molecular docking and dynamics of a dextranase derived from Penicillium cyclopium CICC-4022

This study aimed to investigate the recognition mechanism of dextranase (PC-Edex) produced by Penicillium cyclopium CICC-4022 on dextran. Whole genome information of P. cyclopium CICC-4022 was obtained through genome sequencing technology. The coding information of PC-Edex was determined based on the annotation of the protein-coding genes using protein databases. The three-dimensional structure of PC-Edex was obtained via homology modelling. The active site and binding free energy between PC-Edex and dextran were calculated by molecular docking and molecular dynamics techniques. The results showed that the total sequence length and GC content of P. cyclopium CICC-4022 were 29,710,801 bp and 47.02 %, respectively. The annotation of protein-encoding genes showed that P. cyclopium CICC-4022 is highly active and has many carbohydrate transport and metabolic functions, and most of its proteases are glycolytic anhydrases. Furthermore, the gene encoding PC-Edex was successfully annotated. Molecular dynamics simulations indicated that van der Waals interaction was the main driving force of interaction. Residues Ile114, Asp115, Tyr332, Lys344, and Gln403 significantly promoted the binding between dextran and PC-Edex. In summary, this study explored the active site catalyzed by PC-Edex based on the binding pattern of PC-Edex and dextran. Therefore, this study provides genomic information on dextranase and data supporting the rational modification and enhancement of PC-Edex.

Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting

The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.

Genomic Sequence Resource of Talaromyces albobiverticillius, the Causative Pathogen of Pomegranate Pulp Rot Disease

Talaromyces albobiverticillius, a prominent pathogen responsible for pomegranate pulp rot disease, inflicts significant damage on Punica granatum L. Besides its pathogenicity, this fungus possesses the potential to produce substantial amounts of red pigments, making it promising for industrial applications. This study presents the genome annotation of T. albobiverticillius field strain Tp-2, isolated from pomegranates. The genome assembly, generated through a combination of Oxford Nanopore and Illumina sequencing reads, yielded a high-quality assembly with 14 contigs, featuring an N50 length of 4,594,200 bp. The complete genome of strain Tp-2 spans 38,354,882 bp, with a GC content of 45.78%. Importantly, the assembly exhibits remarkable integrity, with 98.3% of complete Benchmarking Universal Single-Copy Orthologs validating genome completeness. Genome prediction analysis reveals the presence of 10,380 protein-coding genes. To our knowledge, this study is the first report on the genome sequence of T. albobiverticillius, offering valuable insights into its genetic variation and molecular mechanisms of pigment production.

Characteristics of Epicoccum latusicollum as revealed by genomic and metabolic phenomic analysis, the causal agent of tobacco Epicoccus leaf spot

Epicoccum latusicollum is a fungus that causes a severe foliar disease on flue-cured tobacco in southwest China, resulting in significant losses in tobacco yield and quality. To better understand the organism, researchers investigated its optimal growth conditions and metabolic versatility using a combination of traditional methods and the Biolog Phenotype MicroArray technique. The study found that E. latusicollum exhibited impressive metabolic versatility, being able to metabolize a majority of carbon, nitrogen, sulfur, and phosphorus sources tested, as well as adapt to different environmental conditions, including broad pH ranges and various osmolytes. The optimal medium for mycelial growth was alkyl ester agar medium, while oatmeal agar medium was optimal for sporulation, and the optimum temperature for mycelial growth was 25°C. The lethal temperature was 40°C. The study also identified arbutin and amygdalin as optimal carbon sources and Ala-Asp and Ala-Glu as optimal nitrogen sources for E. latusicollum. Furthermore, the genome of E. latusicollum strain T41 was sequenced using Illumina HiSeq and Pacific Biosciences technologies, with 10,821 genes predicted using Nonredundant, Gene Ontology, Clusters of Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and SWISS-PROT databases. Analysis of the metabolic functions of phyllosphere microorganisms on diseased tobacco leaves affected by E. latusicollum using the Biolog Eco microplate revealed an inability to efficiently metabolize a total of 29 carbon sources, with only tween 40 showing some metabolizing ability. The study provides new insights into the structure and function of phyllosphere microbiota and highlights important challenges for future research, as well as a theoretical basis for the integrated control and breeding for disease resistance of tobacco Epicoccus leaf spot. This information can be useful in developing new strategies for disease control and management, as well as enhancing crop productivity and quality.

Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections

BACKGROUND

Secondary bacterial infections and pneumonia are major mortality causes of respiratory viruses, and the disruption of the upper respiratory tract (URT) microbiota is a crucial component of this process. However, whether this URT dysbiosis associates with the viral species (in other words, is viral type-specific) is unclear.

RESULTS

Here, we recruited 735 outpatients with upper respiratory symptoms, identified the infectious virus types in 349 participants using multiplex RT-PCR, and profiled their upper respiratory microbiome using the 16S ribosomal RNA gene and metagenomic gene sequencing. Microbial and viral data were subsequently used as inputs for multivariate analysis aimed at revealing viral type-specific disruption of the upper respiratory microbiota. We found that the oropharyngeal microbiota shaped by influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (RSV), and human rhinovirus (HRV) infections exhibited three distinct patterns of dysbiosis, and Veillonella was identified as a prominent biomarker for any type of respiratory viral infections. Influenza virus infections are significantly correlated with increased oropharynx microbiota diversity and enrichment of functional metabolic pathways such as L-arginine biosynthesis and tetracycline resistance gene tetW. We used the GRiD algorithm and found the predicted growth rate of common respiratory pathogens was increased upon influenza virus infection, while commensal bacteria, such as Streptococcus infantis and Streptococcus mitis, may act as a colonization resistance to the overgrowth of these pathogens.

CONCLUSIONS

We found that respiratory viral infections are linked with viral type-specific disruption of the upper respiratory microbiota, particularly, influenza infections uniquely associated with increased microbial diversity and growth rates of specific pathogens in URT. These findings are essential for clarifying the differences and dynamics of respiratory microbiota in healthy participants and acute respiratory viral infections, which contribute to elucidating the pathogenesis of viral-host-bacterial interactions to provide insights into future studies on effective prevention and treatment of respiratory tract infections. Video Abstract.

Genomic characterization of Pantoea anthophila strain UI705 causing urinary tract infections in China

Introduction

Pantoea anthophila (P. anthophila) is a Gram-negative bacterium initially isolated from Impatiens balsamina in India. P. anthophila has been characterized with low pathogenicity, and no human infections caused by this organism have been reported yet. We report the first case of urinary tract infection caused by P. anthophila in a 73-year-old man after bladder cancer surgery.

Methods

The bacterial isolate gained from urine was named UI705 and identified as P. anthophila by MALDI-TOF mass spectrometry. The genome sequencing and analysis were performed to further characterize the pathogenesis of the clinical isolate.

Result and discussion

To the best of our knowledge, this is the first report of human infection caused by P. anthophila in China. The draft genome sequence of P. anthophila UI705 provides a fundamental resource for subsequent investigation of its virulence factors, antibiotic resistance, host-pathogen interactions, and comparative genomics of genus Pantoea.

A framework for community curation of interspecies interactions literature

The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen-Host Interactions database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology, and controlled vocabularies to curate pathogen-host interaction data, at the level of the host, pathogen, strain, gene, and genotype. The concept of a multispecies genotype, the 'metagenotype,' is introduced to facilitate capturing changes in the disease-causing abilities of pathogens, and host resistance or susceptibility, observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors.

Genome Sequence and Evaluation of Safety and Probiotic Potential of Lactiplantibacillus plantarum LPJZ-658

This study aims to systematically evaluate the safety of a novel L. plantarum LPJZ-658 explored on whole-genome sequence analysis, safety, and probiotic properties assessment. Whole genome sequencing results demonstrated that L. plantarum LPJZ-658 consists of 3.26 Mbp with a GC content of 44.83%. A total of 3254 putative ORFs were identified. Of note, a putative bile saline hydrolase (BSH) (identity 70.4%) was found in its genome. In addition, the secondary metabolites were analyzed, and one secondary metabolite gene cluster was predicted to consist of 51 genes, which verified its safety and probiotic properties at the genome level. Additionally, L. plantarum LPJZ-658 exhibited non-toxic and non-hemolytic activity and was susceptible to various tested antibiotics, indicating that L. plantarum LPJZ-658 was safe for consumption. Moreover, the probiotic properties tests confirm that L. plantarum LPJZ-658 also exhibits tolerance to acid and bile salts, preferably hydrophobicity and auto-aggregation, and excellent antimicrobial activity against both Gram-positive and Gram-negative gastrointestinal pathogens. In conclusion, this study confirmed the safety and probiotic properties of L. plantarum LPJZ-658, suggesting it can be used as a potential probiotic candidate for human and animal applications.

A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome

Stevens-Johnson syndrome (SJS) produces a severe hypersensitivity reaction caused by Herpes simplex virus or mycoplasma infection, vaccination, systemic disease, or other agents. Several studies have investigated the genetic susceptibility involved in SJS. To provide further genetic insights into the pathogenesis of SJS, this study prioritized high-impact, SJS-associated pathogenic variants through integrating bioinformatic and population genetic data. First, we identified SJS-associated single nucleotide polymorphisms from the genome-wide association studies catalog, followed by genome annotation with HaploReg and variant validation with Ensembl. Subsequently, expression quantitative trait locus (eQTL) from GTEx identified human genetic variants with differential gene expression across human tissues. Our results indicate that two variants, namely rs2074494 and rs5010528, which are encoded by the HLA-C (human leukocyte antigen C) gene, were found to be differentially expressed in skin. The allele frequencies for rs2074494 and rs5010528 also appear to significantly differ across continents. We highlight the utility of these population-specific HLA-C genetic variants for genetic association studies, and aid in early prognosis and disease treatment of SJS.

Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata

BACKGROUND

Armillaria species are plant pathogens, but a few Armillaria species can establish a symbiotic relationship with Gastrodia elata, a rootless and leafless orchid, that is used as a Chinese herbal medicine. Armillaria is a nutrient source for the growth of G. elata. However, there are few reports on the molecular mechanism of symbiosis between Armillaria species and G. elata. The genome sequencing and analysis of Armillaria symbiotic with G. elata would provide genomic information for further studying the molecular mechanism of symbiosis.

RESULTS

The de novo genome assembly was performed with the PacBio Sequel platform and Illumina NovaSeq PE150 for the A. gallica Jzi34 strain, which was symbiotic with G. elata. Its genome assembly contained ~ 79.9 Mbp and consisted of 60 contigs with an N50 of 2,535,910 bp. There were only 4.1% repetitive sequences in the genome assembly. Functional annotation analysis revealed a total of 16,280 protein coding genes. Compared with the other five genomes of Armillaria, the carbohydrate enzyme gene family of the genome was significantly contracted, while it had the largest set of glycosyl transferase (GT) genes. It also had an expansion of auxiliary activity enzymes AA3-2 gene subfamily and cytochrome P450 genes. The synteny analysis result of P450 genes reveals that the evolutionary relationship of P450 proteins between A. gallica Jzi34 and other four Armillaria was complex.

CONCLUSIONS

These characteristics may be beneficial for establishing a symbiotic relationship with G. elata. These results explore the characteristics of A. gallica Jzi34 from a genomic perspective and provide an important genomic resource for further detailed study of Armillaria. This will help to further study the symbiotic mechanism between A. gallica and G. elata.

Kosakonia radicincitans with hypervirulent lON genes causes human bloodstream infections

Kosakonia radicincitans is a species within the new genus Kosakonia, which is typically a plant pathogen, with rare reports of human infection. The number of human infections may be underestimated because this new genus is under-represented among diagnostic tools. This report describes a case of bloodstream infection caused by K. radicincitans. The pathogen was identified by matrix-assisted laser desorption/ionization-TOF mass spectrometry and 16S rRNA gene sequencing. The hypervirulent human pathogenicity gene LON, which has not been described before, was detected in the bacterial genome by gene annotation. Thus, this discovery provides a new reference for studying the pathogenic mechanism of this rare pathogen.

Complete genome analysis of pathogenic Metschnikowia bicuspidata strain MQ2101 isolated from diseased ridgetail white prawn, Exopalaemon carinicauda

BACKGROUND

Metschnikowia bicuspidata is a pathogenic yesst that can cause disease in many different economic aquatic animal species. In recent years, there was a new disease outbreak in ridgetail white prawn (Exopalaemon carinicauda) in coastal areas of Jiangsu Province China that was referred to as zombie disease by local farmers. The pathogen was first isolated and identified as M. bicuspidata. Although the pathogenicity and pathogenesis of this pathogen in other animals have been reported in some previous studies, research on its molecular mechanisms is still very limited. Therefore, a genome-wide study is necessary to better understand the physiological and pathogenic mechanisms of M. bicuspidata.

RESULT

In this study, we obtained a pathogenic strain, MQ2101, of M. bicuspidata from diseased E. carinicauda and sequenced its whole genome. The size of the whole genome was 15.98 Mb, and it was assembled into 5 scaffolds. The genome contained 3934 coding genes, among which 3899 genes with biological functions were annotated in multiple underlying databases. In KOG database, 2627 genes were annotated, which were categorized into 25 classes including general function prediction only, posttranslational modification, protein turnover, chaperones, and signal transduction mechanisms. In KEGG database, 2493 genes were annotated, which were categorized into five classes, including cellular processes, environmental information processing, genetic information processing, metabolism and organismal systems. In GO database, 2893 genes were annotated, which were mainly classified in cell, cell part, cellular processes and metabolic processes. There were 1055 genes annotated in the PHI database, accounting for 26.81% of the total genome, among which 5 genes were directly related to pathogenicity (identity ≥ 50%), including hsp90, PacC, and PHO84. There were also some genes related to the activity of the yeast itself that could be targeted by antiyeast drugs. Analysis based on the DFVF database showed that strain MQ2101 contained 235 potential virulence genes. BLAST searches in the CAZy database showed that strain MQ2101 may have a more complex carbohydrate metabolism system than other yeasts of the same family. In addition, two gene clusters and 168 putative secretory proteins were predicted in strain MQ2101, and functional analysis showed that some of the secretory proteins may be directly involved in the pathogenesis of the strain. Gene family analysis with five other yeasts revealed that strain MQ2101 has 245 unique gene families, including 274 genes involved in pathogenicity that could serve as potential targets.

CONCLUSION

Genome-wide analysis elucidated the pathogenicity-associated genes of M. bicuspidate while also revealing a complex metabolic mechanism and providing putative targets of action for the development of antiyeast drugs for this pathogen. The obtained whole-genome sequencing data provide an important theoretical basis for transcriptomic, proteomic and metabolic studies of M. bicuspidata and lay a foundation for defining its specific mechanism of host infestation.

Whole-Genome Sequencing of Fusarium oxysporum f. sp. cucumerinum Strain Race-4 Infecting Cucumber in China

Fusarium oxysporum f. sp. cucumerinum, which causes root and vascular wilting, is one of the most devastating diseases infecting cucumber. Here, we report the first genome resource with high-quality assembly for F. oxysporum f. sp. cucumerinum strain Race-4, which is primarily endemic to China. The genome was 59.11 Mb in size and consisted of 48 scaffolds with an N50 of 3.87 Mb using PacBio long reads (301.77×) sequencing, and encodes 14,898 proteins from analyzing RNA-seq data. Gene annotations identified pathogen-host interaction genes, fungal virulence factors, secreted proteins, transcription factors, and secondary metabolite biosynthesis gene. Moreover, functional genes reported in previous studies were also identified in the genome of Race-4. These genes and genome resource may play important roles in understanding F. oxysporum f. sp. cucumerinum-cucumber interactions and will be useful for further research.

Characterization and Genome Analysis of Cladobotryum mycophilum, the Causal Agent of Cobweb Disease of Morchella sextelata in China

Cobweb disease is a fungal disease that can cause serious damage to edible mushrooms worldwide. To investigate cobweb disease in Morchella sextelata in Guizhou Province, China, we isolated and purified the pathogen responsible for the disease. Through morphological and molecular identification and pathogenicity testing on infected M. sextelata, we identified Cladobotryum mycophilum as the cause of cobweb disease in this region. This is the first known occurrence of this pathogen causing cobweb disease in M. sextelata anywhere in the world. We then obtained the genome of C. mycophilum BJWN07 using the HiFi sequencing platform, resulting in a high-quality genome assembly with a size of 38.56 Mb, 10 contigs, and a GC content of 47.84%. We annotated 8428 protein-coding genes in the genome, including many secreted proteins, host interaction-related genes, and carbohydrate-active enzymes (CAZymes) related to the pathogenesis of the disease. Our findings shed new light on the pathogenesis of C. mycophilum and provide a theoretical basis for developing potential prevention and control strategies for cobweb disease.

Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics

Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact on reproductive health, the widespread presence of antimicrobial resistance, and the lack of a vaccine. In this study, we used a bioinformatics approach and performed subtractive genomic methods to identify potential drug targets against the core proteome of N. gonorrhoeae (12 strains). In total, 12,300 protein sequences were retrieved, and paralogous proteins were removed using CD-HIT. The remaining sequences were analyzed for non-homology against the human proteome and gut microbiota, and screened for broad-spectrum analysis, druggability, and anti-target analysis. The proteins were also characterized for unique interactions between the host and pathogen through metabolic pathway analysis. Based on the subtractive genomic approach and subcellular localization, we identified one cytoplasmic protein, 2Fe-2S iron-sulfur cluster binding domain-containing protein (NGFG RS03485), as a potential drug target. This protein could be further exploited for drug development to create new medications and therapeutic agents for the treatment of N. gonorrhoeae infections.

Whole genome sequence of Cryptosphaeria pullmanensis, an important pathogenic fungus potentially threatening crop and forestry production

Many fungal members of the Diatrypaceae family are pathogenic towards plants and are widely distributed globally. Cryptosphaeria pullmanensis is a pathogenic fungus that infects populus and walnut trees, causing their death. We sequenced the genome of C. pullmanensis based on a combination of Nanopore PromethION and Illumina NovaSeq PE150 platforms, and functionally annotated the sequences using a number of open-access databases. This is the first report of the genome-scale assembly and annotation for C. pullmanensis, the first species of the genus Cryptosphaeria to be sequenced. We obtained 13 contigs with an N50 contig size of 7,095,780 bp, a GC content ratio of 43.23% and a genome size of 56.72 Mb with 10,474 putative coding genes. Comparative genomic analysis against the genomes of seven Ascomycetes fungal strains was performed. Among the seven species tested, the Eutypa lata genome displayed the highest similarity to the C. pullmanensis genome in terms of collinearity and homologous gene content. This study has provided a genetic resource that offers extensive information and a framework for future investigations into the transcriptome, proteome, and metabonome of C. pullmanensis to understand its molecular pathogenesis.

Genome Sequence Resource of Fusarium proliferatum f. sp. malus domestica MR5, the Causative Agent of Apple Replant Disease

Apple replant disease (ARD) caused by the fungal pathogen Fusarium proliferatum f. sp. malus domestica (Fpmd) MR5 brings annual losses to apple production within China. However, the genomic information of the pathogen is not yet available. Here, we obtained the whole-genome sequence of the highly virulent Fpmd MR5 using the Illumina PE150 platform. The genome size was 42.76 Mb and consisted of 9,047 genes. The GC content was 48.80%, and several genes potentially associated with pathogenicity were identified, such as carbohydrate-active enzymes, secreted proteins, and secondary metabolite gene clusters. There were 260 specific virulence factor genes, mainly related to fungal vegetative growth and the production of cell wall-degrading enzymes. These data will aid future studies investigating host-pathogen interactions and help us develop suitable disease management strategies.

Virulence-Associated Genes of Calonectria ilicola, Responsible for Cylindrocladium Black Rot

The Cylindrocladium black rot caused by Calonectria ilicicola is a destructive disease affecting a broad range of crops. Herein, we study virulence-associated genes of C. ilicicolaCi14017 isolated from diseased peanut roots (Arachis hypogaea L.). Ci14017 was identified via phylogenetic analysis of the internal transcribed spacer region and standard Koch’s postulate testing. Virulence-associated genes were based on genome analyses and comparative analysis of transcriptome and proteome profiles of sensitive and resistant peanut cultivars. Ci14017 identified as C. ilicicola has a 66 Mb chromosome with 18,366 predicted protein-coding genes. Overall, 46 virulence-associated genes with enhanced expression levels in the sensitive cultivars were identified. Sequence analysis indicated that the 46 gene products included two merops proteins, eight carbohydrate-active enzymes, seven cytochrome P450 enzymes, eight lipases, and 20 proteins with multi-conserved enzyme domains. The results indicate a complex infection mechanism employed by Ci14017 for causing Cylindrocladium black rot in peanuts.

Diplodia tip blight pathogen's virulence empowered through host switch

Increased drought combined with emerging pathogens poses an increased threat to forest health. This is attributable to the unpredictable behaviour of forest pathosystems, which can favour fungal pathogens over the host under persistent drought stress conditions. Diplodia sapinea (≡ Sphaeropsis sapinea) is one of the most severe pathogens in Scots pine (Pinus sylvestris) causing Diplodia tip blight (conifer blight) under certain environmental conditions. Recently, the fungus has also been isolated from non-conifer hosts, indicating that it has a broader host range than previously known. In this study we compared the impact of different levels of water availability on necrosis length caused by D. sapinea strains isolated as endophytes (eight strains isolated from asymptomatic Scots pine) and pathogens (five strains isolated from symptomatic Scots pine) and five strains isolated from symptomatic non-pine hosts. For all strains the decreased water availability increased the necrosis length in Scots pine shoots. The isolates from non-pine hosts caused the most severe reactions under all water availabilities. The results of the study indicate the likelihood that effects of climatic changes such as drought will drive D. sapinea damage in Scots pine-dominated forests and increase mortality rates in affected trees. Further, the higher necrosis in the Scots pines caused by strains that had performed a host switch are concerning with regard to future scenarios thus increasing infection pressure on Scots pine from unknown sources.

Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses

Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes.

Bioinformatics strategies for studying the molecular mechanisms of fungal extracellular vesicles with a focus on infection and immune responses

Fungal extracellular vesicles (EVs) are released during pathogenesis and are found to be an opportunistic infection in most cases. EVs are immunocompetent with their host and have paved the way for new biomedical approaches to drug delivery and the treatment of complex diseases including cancer. With computing and processing advancements, the rise of bioinformatics tools for the evaluation of various parameters involved in fungal EVs has blossomed. In this review, we have complied and explored the bioinformatics tools to analyze the host-pathogen interaction, toxicity, omics and pathogenesis with an array of specific tools that have depicted the ability of EVs as vector/carrier for therapeutic agents and as a potential theme for immunotherapy. We have also discussed the generation and pathways involved in the production, transport, pathogenic action and immunological interactions of EVs in the host system. The incorporation of network pharmacology approaches has been discussed regarding fungal pathogens and their significance in drug discovery. To represent the overview, we have presented and demonstrated an in silico study model to portray the human Cryptococcal interactions.

PHILM2Web: A high-throughput database of macromolecular host–pathogen interactions on the Web

During infection, the pathogen’s entry into the host organism, breaching the host immune defense, spread and multiplication are frequently mediated by multiple interactions between the host and pathogen proteins. Systematic studying of host–pathogen interactions (HPIs) is a challenging task for both experimental and computational approaches and is critically dependent on the previously obtained knowledge about these interactions found in the biomedical literature. While several HPI databases exist that manually filter HPI protein–protein interactions from the generic databases and curated experimental interactomic studies, no comprehensive database on HPIs obtained from the biomedical literature is currently available. Here, we introduce a high-throughput literature-mining platform for extracting HPI data that includes the most comprehensive to date collection of HPIs obtained from the PubMed abstracts. Our HPI data portal, PHILM2Web (Pathogen–Host Interactions by Literature Mining on the Web), integrates an automatically generated database of interactions extracted by PHILM, our high-precision HPI literature-mining algorithm. Currently, the database contains 23 581 generic HPIs between 157 host and 403 pathogen organisms from 11 609 abstracts. The interactions were obtained from processing 608 972 PubMed abstracts, each containing mentions of at least one host and one pathogen organisms. In response to the coronavirus disease 2019 (COVID-19) pandemic, we also utilized PHILM to process 25 796 PubMed abstracts obtained by the same query as the COVID-19 Open Research Dataset. This COVID-19 processing batch resulted in 257 HPIs between 19 host and 31 pathogen organisms from 167 abstracts. The access to the entire HPI dataset is available via a searchable PHILM2Web interface; scientists can also download the entire database in bulk for offline processing.

Database URL: http://philm2web.live

Genome sequence and pathogenicity of Vibrio vulnificus strain MCCC 1A08743 isolated from contaminated prawns

Vibrio vulnificus is an opportunistic pathogen that naturally inhabits sea water globally and is responsible for most vibriosis-related deaths. The consumption of V. vulnificus contaminated seafood and exposure of wounds to Vibrio can result in systemic infection, with increased risks of amputation and extremely high rates of mortality. However, the pathogenicity and virulence factors of V. vulnificus are not fully understood. The genomic characterization of V. vulnificus will be helpful to extend our understanding on V. vulnificus at a genomic level. In this manuscript, the genome of V. vulnificus strain MCCC 1A08743 isolated from contaminated prawns from Zhanjiang, China, was sequenced using Illumina HiSeq X Ten system and annotated through multiple databases. The strain MCCC 1A08743 genome included 4371 protein-coding genes and 117 RNA genes. Average nucleotide identity analysis and core genome phylogenetic analysis revealed that MCCC 1A08743 was most closely related to strains from clinical samples from the United States. Pathogenicity annotation of the MCCC 1A08743 genome, using Virulence Factor Database and Pathogen-Host Interactions database, predicted the pathogenicity of the strain, and this was confirmed using mice infection experiments, which indicated that V. vulnificus strain MCCC 1A08743 could infect C57BL/6J mice and cause liver lesions.

This article has an associated First Person interview with the first author of the paper.

Summary:Vibrio vulnificus strain MCCC 1A08743 was newly isolated, sequenced and tested for its pathogenicity in mice.

Identification of functional genes associated with the biotransformation of limonene to trans-dihydrocarvone in Klebsiella sp. O852

BACKGROUND

Natural dihydrocarvone has been widely used in the food, cosmetics, agrochemicals and pharmaceuticals industries because of its sensory properties and physiological effects. In our previous study, Klebsiella sp. O852 was shown to be capable of converting limonene to trans-dihydrocarvone with high catalytic efficiency. Thus, it was essential to identify and characterize the functional genes involved in limonene biotransformation using genome sequencing and heterologous expression.

RESULTS

The 5.49-Mb draft genome sequence of Klebsiella sp. O852 contained 5218 protein-encoding genes. Seven candidate genes participating in the biotransformation of limonene to trans-dihydrocarvone were identified by genome analysis. Heterologous expression of these genes in Escherichia coli BL21(DE3) indicated that 0852_GM005124 and 0852_GM003417 could hydroxylate limonene in the six position to yield carveol, carvone and trans-dihydrocarvone. 0852_GM002332 and 0852_GM001602 could catalyze the oxidation of carveol to carvone and trans-dihydrocarvone. 0852_GM000709, 0852_GM001600 and 0852_GM000954 had high carvone reductase activity toward the hydrogenation of carvone to trans-dihydrocarvone.

CONCLUSION

The results obtained in the present study suggest that the seven genes described above were responsible for converting limonene to trans-dihydrocarvone. The present study contributes to providing a foundation for the industrial production of trans-dihydrocarvone in microbial chassis cells using synthetic biology strategies. © 2021 Society of Chemical Industry.

Complete Genome Analysis of Highly Pathogenic Non-O1/O139 Vibrio cholerae Isolated From Macrobrachium rosenbergii Reveals Pathogenicity and Antibiotic Resistance-Related Genes

Non-O1/O139 Vibrio cholerae is a highly virulent pathogen that causes mass mortalities of various aquatic animals. In the present study, we sequenced the whole genome of non-O1/O139 V. cholerae GXFL1-4, isolated from Macrobrachium rosenbergii, to reveal the pathogenicity and antibiotic resistance. The result showed its genome contained two circular chromosomes and one plasmid with a total size of 4,282,243 bp, which harbored 3,869 coding genes. Among them, 3,047, 2,659, and 3,661 genes were annotated in the Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. In addition, 372 potential virulence genes were predicted based on the Virulence Factor Database (VFDB) database, such as type II, III, IV, and VI secretion systems related genes, flagella genes, and pilus formation or motility-related genes. Blast results in the Comprehensive Antibiotic Resistance Database (CARD) database showed that the strain contained 148 antibiotic resistance-related genes belonging to 27 categories, such as efflux pump complex antibiotic resistance genes and antibiotic resistance gene cluster genes. The Pathogen-Host Interaction (PHI) database annotated 320 genes related to pathogen-host interaction, such as T3SS, virulence regulatory factors, transcriptional regulators, and two-component response regulator related genes. The whole-genome analysis suggested that the pathogenic non-O1/O139 V. cholerae strain GXFL1-4 might have a complex molecular mechanism of pathogenicity and antibiotic resistance. This study provides a wealth of information about non-O1/O139 V. cholerae genes related to its pathogenicity and drug resistance and will facilitate the understanding of its pathogenesis as well as the development of prevention and treatment strategies for the pathogen.

The First Whole Genome Sequence Discovery of the Devastating Fungus Arthrinium rasikravindrae

Devastating fungi are one of the most important biotic factors associated with numerous infectious diseases not only in plants but in animals and humans too. Arthrinium rasikravindrae a devastating fungus is responsible for severe infections in a large number of host plants all over the world. In the present study, we analyzed the whole genome sequence of devastating fungus A. rasikravindrae strain AQZ-20, using Illumina Technology from the Novogene Bio-informatics Co., Ltd. Beijing, China. To identify associated annotation results, various corresponding functional annotations databases were utilized. The genome size was 48.24 MB with an N90 (scaffolds) length of 2,184,859 bp and encoded putative genes were 11,101, respectively. In addition, we evaluated the comparative genomic analyses with 4 fungal strains of Ascomycetes. Two related species showed a strong correlation while others exhibited a weak correlation with the A. rasikravindrae AQZ-20 fungus. This study is a discovery of the genome-scale assembly, as well as annotation for A. rasikravindrae. The results obtained from the whole genome sequencing and genomic resources developed in this study will contribute significantly to genetic improvement applications against diseases caused by A. rasikravindrae. In addition, the phylogenetic tree, followed by genomic RNA, transcriptomic, proteomic, metabolic, as well as pathogenic data reported in current research will provide deep insight for further studies in the future.

Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence

Guava wilt disease is caused by the fungus Nalanthamala psidii. The wilt disease results in large-scale destruction of orchards in South Africa, Taiwan, and several Southeast Asian countries. De novo assembly, annotation, and in-depth analysis of the N. psidii genome were carried out to facilitate the identification of characteristics associated with pathogenicity and pathogen evolution. The predicted secretome revealed a range of CAZymes, proteases, lipases and peroxidases associated with plant cell wall degradation, nutrient acquisition, and disease development. Further analysis of the N. psidii carbohydrate-active enzyme profile exposed the broad-spectrum necrotrophic lifestyle of the pathogen, which was corroborated by the identification of putative effectors and secondary metabolites with the potential to induce tissue necrosis and cell surface-dependent immune responses. Putative regulatory proteins including transcription factors and kinases were identified in addition to transporters potentially involved in the secretion of secondary metabolites. Transporters identified included important ABC and MFS transporters involved in the efflux of fungicides. Analysis of the repetitive landscape and the detection of mechanisms linked to reproduction such as het and mating genes rendered insights into the biological complexity and evolutionary potential of N. psidii as guava pathogen. Hence, the assembly and annotation of the N. psidii genome provided a valuable platform to explore the pathogenic potential and necrotrophic lifestyle of the guava wilt pathogen.

Genomic signatures and insights into host niche adaptation of the entomopathogenic fungus Metarhizium humberi

The genus Metarhizium is composed of species used in biological control programs of agricultural pests worldwide. This genus includes common fungal pathogen of many insects and mites and endophytes that can increase plant growth. Metarhizium humberi was recently described as a new species. This species is highly virulent against some insect pests and promotes growth in sugarcane, strawberry, and soybean crops. In this study, we sequenced the genome of M. humberi, isolate ESALQ1638, and performed a functional analysis to determine its genomic signatures and highlight the genes and biological processes associated with its lifestyle. The genome annotation predicted 10633 genes in M. humberi, of which 92.0% are assigned putative functions, and ∼17% of the genome was annotated as repetitive sequences. We found that 18.5% of the M. humberi genome is similar to experimentally validated proteins associated with pathogen-host interaction. Compared to the genomes of eight Metarhizium species, the M. humberi ESALQ1638 genome revealed some unique traits that stood out, e.g., more genes functionally annotated as polyketide synthases (PKSs), overrepresended GO-terms associated to transport of ions, organic and amino acid, a higher percentage of repetitive elements, and higher levels of RIP-induced point mutations. The M. humberi genome will serve as a resource for promoting studies on genome structure and evolution that can contribute to research on biological control and plant biostimulation. Thus, the genomic data supported the broad host range of this species within the generalist PARB clade and suggested that M. humberi ESALQ1638 might be particularly good at producing secondary metabolites and might be more efficient in transporting amino acids and organic compounds.

Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709

Over the past decade, Apiotrichum mycotoxinivorans has been recognized globally as a source of opportunistic infections. It is a yeast-like fungus, and its association as an uncommon pulmonary pathogen with cystic fibrosis patients has been previously reported. Immunocompromised patients are at the highest risk of A. mycotoxinivorans infections. Therefore, to investigate the genetic basis for the pathogenicity of A. mycotoxinivorans, we performed whole-genome sequencing and comparative genomic analysis of A. mycotoxinivorans GMU1709 that was isolated from sputum specimens of a pneumonia patient receiving cardiac repair surgery. The assembly of Oxford Nanopore reads from the GMU1709 strain and its subsequent correction using Illumina paired-end reads yielded a high-quality complete genome with a genome size of 30.5 Mb in length, which comprised six chromosomes and one mitochondrion. Subsequently, 8,066 protein-coding genes were predicted based on multiple pieces of evidence, including transcriptomes. Phylogenomic analysis indicated that A. mycotoxinivorans exhibited the closest evolutionary affinity to A. veenhuisii, and both the A. mycotoxinivorans strains and the formerly Trichosporon cutaneum ACCC 20271 strain occupied the same phylogenetic position. Further comparative analysis supported that the ACCC 20271 strain belonged to A. mycotoxinivorans. Comparisons of three A. mycotoxinivorans strains indicated that the differences between clinical and non-clinical strains in pathogenicity and drug resistance may be little or none. Based on the comparisons with strains of other species in the Trichosporonaceae family, we identified potential key genetic factors associated with A. mycotoxinivorans infection or pathogenicity. In addition, we also deduced that A. mycotoxinivorans had great potential to inactivate some antibiotics (e.g., tetracycline), which may affect the efficacy of these drugs in co-infection. In general, our analyses provide a better understanding of the classification and phylogeny of the Trichosporonaceae family, uncover the underlying genetic basis of A. mycotoxinivorans infections and associated drug resistance, and provide clues into potential targets for further research and the therapeutic intervention of infections.

Two Novel Dimorphism-Related Virulence Factors of Zymoseptoria tritici Identified Using Agrobacterium-Mediated Insertional Mutagenesis

Diseases caused by dimorphic phytopathogenic and systemic dimorphic fungi have markedly increased in prevalence in the last decades, and understanding the morphogenic transition to the virulent state might yield novel means of controlling dimorphic fungi. The dimorphic fungus Z. tritici causes significant economic impact on wheat production, and yet the regulation of the dimorphic switch, a key first step in successful plant colonization, is still largely unexplored in this fungus. The fungus is amenable to suppression by fungicides at this switch point, and the identification of the factors controlling the dimorphic switch provides a potential source of novel targets to control Septoria tritici blotch (STB). Inhibition of the dimorphic switch can potentially prevent penetration and avoid any damage to the host plant. The aim of the current work was to unveil genetic determinants of the dimorphic transition in Z. tritici by using a forward genetics strategy. Using this approach, we unveiled two novel factors involved in the switch to the pathogenic state and used reverse genetics and complementation to confirm the role of the novel virulence factors and further gained insight into the role of these genes, using transcriptome analysis via RNA-Seq. The transcriptomes generated potentially contain key determinants of the dimorphic transition.