scholarly journals Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in thePseudomonas syringaespecies complex

2017 ◽  
Author(s):  
Marcus M. Dillon ◽  
Shalabh Thakur ◽  
Renan N.D. Almeida ◽  
David S. Guttman
Keyword(s):  
Pseudomonas Syringae ◽  
Species Complex ◽  
Bacterial Species ◽  
Orthologous Gene ◽  
Gene Families ◽  
Biological Species ◽  
Genetic Exchange ◽  
Crop Species ◽  
Pan Genome ◽  
Wide Range

ABSTRACTPseudomonas syringaeis a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crop species. Here, we examine the evolutionary relationships of 391 agricultural and environmental strains from theP. syringaespecies complex using whole-genome sequencing and evolutionary genomic analyses. Our collection includes strains from 11 of the 13 previously described phylogroups isolated off of over 90 hosts. We describe the phylogenetic distribution of all orthologous gene families in theP. syringaepan-genome, reconstruct the phylogeny ofP. syringaeusing a core genome alignment and a hierarchical clustering analysis of pan-genome content, predict ecologically and evolutionary relevant loci, and establish the forces of molecular evolution operating on each gene family. We find that the common ancestor of the species complex likely carried a Rhizobium-like type III secretion system (TTSS) and later acquired the canonical TTSS. The phylogenetic analysis also showed that the species complex is subdivided into primary and secondary phylogroups based on genetic diversity and rates of genetic exchange. The primary phylogroups, which largely consist of agricultural isolates, are no more divergent than a number of other bacterial species, while the secondary phylogroups, which largely consists of environmental isolates, have levels of diversity more in line with multiple distinct species within a genus. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also found that “ecologically significant” virulence-associated loci and “evolutionary significant” loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange. These results indicate that while inter-phylogroup recombination occurs relatively rarely in the species complex, it is an important force of genetic cohesion, particularly among the strains in the primary phylogroups. This level of genetic cohesion and the shared plant-associated niche argues for considering the primary phylogroups as a true biological species.

scholarly journals First Steps in the Analysis of Prokaryotic Pan-Genomes

2020 ◽  
Vol 14 ◽  
pp. 117793222093806
Author(s):  
Sávio Souza Costa ◽  
Luís Carlos Guimarães ◽  
Artur Silva ◽  
Siomar Castro Soares ◽  
Rafael Azevedo Baraúna
Keyword(s):  
Genome Analysis ◽  
Core Genome ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Specific Group ◽  
The Core ◽  
Pan Genome ◽  
Research Areas ◽  
Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

scholarly journals The barley pan-genome reveals the hidden legacy of mutation breeding

Nature ◽  
2020 ◽  
Vol 588 (7837) ◽  
pp. 284-289 ◽  
Author(s):  
Murukarthick Jayakodi ◽  
Sudharsan Padmarasu ◽  
Georg Haberer ◽  
Venkata Suresh Bonthala ◽  
Heidrun Gundlach ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Mutation Breeding ◽  
Climatic Conditions ◽  
Crop Species ◽  
Genomic Structural Variation ◽  
Pan Genome ◽  
Wide Range ◽  
Full Complement ◽  
High Quality Sequence ◽  
Barley Germplasm

AbstractGenetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

scholarly journals PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

GigaScience ◽  
2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Sion C Bayliss ◽  
Harry A Thorpe ◽  
Nicola M Coyle ◽  
Samuel K Sheppard ◽  
Edward J Feil
Keyword(s):  
Allelic Variation ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Orthologous Gene ◽  
Gene Families ◽  
Iterative Refinement ◽  
Bacterial Populations ◽  
Sequencing Technologies ◽  
Wide Range ◽  
Similarity Thresholds

Abstract Background Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets. Results Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family. Conclusions We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.

scholarly journals PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

2019 ◽  
Author(s):  
Sion C. Bayliss ◽  
Harry A. Thorpe ◽  
Nicola M. Coyle ◽  
Samuel K. Sheppard ◽  
Edward J. Feil
Keyword(s):  
Allelic Variation ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Orthologous Gene ◽  
Gene Families ◽  
Iterative Refinement ◽  
Supplementary Information ◽  
Bacterial Populations ◽  
Wide Range ◽  
Or Gene

AbstractCataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement And Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds and uses the clustering information to rapidly classify paralogous gene families into either putative fission/fusion events or gene duplications. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation and estimates sequence divergence for each gene family. We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.AvailabilityPIRATE is implemented in Perl and is freely available under an GNU GPL 3 open source license fromhttps://github.com/SionBayliss/PIRATE.Supplementary InformationSupplementary data is available online.

scholarly journals Variation at the common polysaccharide antigen locus drives lipopolysaccharide diversity within the P. syringae species complex

2020 ◽  
Author(s):  
Jay Jayaraman ◽  
William T. Jones ◽  
Dawn Harvey ◽  
Lauren M. Hemara ◽  
Honour C. McCann ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Species Complex ◽  
Allelic Variation ◽  
Gene Knockout ◽  
Genetic Locus ◽  
Core Gene ◽  
Polysaccharide Antigen ◽  
Wide Range ◽  
The Common ◽  
Immunogenic Properties

ABSTRACTThe common polysaccharide antigen (CPA) from the lipopolysaccharide (LPS) component of cell walls from the species complex Pseudomonas syringae is highly variable both in structure and immunological specificity, but the genetic basis for this is not well understood. We have characterised the CPA locus from P. syringae pv. actinidiae (Psa). This locus has a modular structure with genes for both L- and D- rhamnose (Rha) biosynthesis and that of an unknown sugar. It also contains an operon coding for ABC transporter subunits, a bifunctional glycosyltransferase and an O-methyltransferase. This operon is predicted to have a role in transport, elongation and termination of the Rha backbone of the CPA oligosaccharide and is referred to as the TET operon. This is the first report of the identification of this operon in P. syringae. Two alleles of the TET operon were present amongst the different biovars of Psa and lineages of the closely related pathovar P. syringae pv. actinidifoliorum. This allelic variation was reflected in the electrophoretic properties of purified LPS from the different isolates. Gene knockout of the TET operon allele from biovar 1 and replacement with that from biovar 3, demonstrated the link between the genetic locus and the electrophoretic and immunogenic properties of the LPS molecules in Psa. Sequence analysis of the TET operon from a wide range of P. syringae and P. viridiflava isolates displayed a phylogenetic history which is incongruent with core gene phylogeny, but correlates with previously reported tailocin sensitivity, suggesting a functional relationship between LPS structure and tailocin susceptibility.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

scholarly journals Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
John T. Lovell ◽  
Nolan B. Bentley ◽  
Gaurab Bhattarai ◽  
Jerry W. Jenkins ◽  
Avinash Sreedasyam ◽  
...  
Keyword(s):  
Tree Breeding ◽  
Pathogen Resistance ◽  
Perennial Crop ◽  
Crop Species ◽  
Annotation Database ◽  
Pan Genome ◽  
Genome Integration ◽  
Transformative Potential ◽  
Genome Assemblies ◽  
Quantitative Genomics

AbstractGenome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

scholarly journals Silicon Effects on the Root System of Diverse Crop Species Using Root Phenotyping Technology

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 885
Author(s):  
Pooja Tripathi ◽  
Sangita Subedi ◽  
Abdul Latif Khan ◽  
Yong-Suk Chung ◽  
Yoonha Kim
Keyword(s):  
Root System ◽  
Root Morphology ◽  
Morphological Traits ◽  
Crop Production ◽  
Spatial Configuration ◽  
Global Climate ◽  
Learning Technologies ◽  
Climate Change Scenarios ◽  
Crop Species ◽  
Wide Range

Roots play an essential function in the plant life cycle, as they utilize water and essential nutrients to promote growth and plant productivity. In particular, root morphology characteristics (such as length, diameter, hairs, and lateral growth) and the architecture of the root system (spatial configuration in soil, shape, and structure) are the key elements that ensure growth and a fine-tuned response to stressful conditions. Silicon (Si) is a ubiquitous element in soil, and it can affect a wide range of physiological processes occurring in the rhizosphere of various crop species. Studies have shown that Si significantly and positively enhances root morphological traits, including root length in rice, soybean, barley, sorghum, mustard, alfalfa, ginseng, and wheat. The analysis of these morphological traits using conventional methods is particularly challenging. Currently, image analysis methods based on advanced machine learning technologies allowed researchers to screen numerous samples at the same time considering multiple features, and to investigate root functions after the application of Si. These methods include root scanning, endoscopy, two-dimensional, and three-dimensional imaging, which can measure Si uptake, translocation and root morphological traits. Small variations in root morphology and architecture can reveal different positive impacts of Si on the root system of crops, with or without exposure to stressful environmental conditions. This review comprehensively illustrates the influences of Si on root morphology and root architecture in various crop species. Furthermore, it includes recommendations in regard to advanced methods and strategies to be employed to maintain sustainable plant growth rates and crop production in the currently predicted global climate change scenarios.

scholarly journals Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

2021 ◽  
Vol 9 (4) ◽  
pp. 862
Author(s):  
Vittoria Catara ◽  
Jaime Cubero ◽  
Joël F. Pothier ◽  
Eran Bosis ◽  
Claude Bragard ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Bacterial Species ◽  
Management Strategies ◽  
Diagnostic Methods ◽  
Plant Diseases ◽  
Wild Plants ◽  
Future Climate Change ◽  
Climate Change Scenarios ◽  
Wide Range ◽  
Diversity Studies

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

scholarly journals Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Hannes Petruschke ◽  
Christian Schori ◽  
Sebastian Canzler ◽  
Sarah Riesbeck ◽  
Anja Poehlein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Intestinal Microbiota ◽  
De Novo ◽  
Bacterial Species ◽  
Intestinal Microbiome ◽  
Single Strain ◽  
Small Proteins ◽  
Human Intestinal Microbiota ◽  
Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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