CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic

Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular targets of clinical interventions

Primordial origin and diversification of plasmids in Lyme disease agent bacteria

Abstract Background: With approximately one-third of their genomes consisting of linear and circular plasmids, the Lyme disease agent cluster of species has the most complex genomes among known bacteria. We report here a comparative analysis of plasmids in eleven Borreliella (also known as Borrelia burgdorferi sensu lato) species. Results: We sequenced the complete genomes of two B. afzelii, two B. garinii, and individual B. spielmanii, B. bissettiae, B. valaisiana and B. finlandensis isolates. These individual isolates carry between seven and sixteen plasmids, and together harbor 99 plasmids. We report here a comparative analysis of these plasmids, along with 70 additional Borreliella plasmids available in the public sequence databases. We identify only one new putative plasmid compatibility type (the 30th) among these 169 plasmid sequences, suggesting that all or nearly all such types have now been discovered. We find that the linear plasmids in the non-B. burgdorferi species have undergone the same kinds of apparently random, chaotic rearrangements mediated by non-homologous recombination that we previously discovered in B. burgdorferi. These rearrangements occurred independently in the different species lineages, and they, along with an expanded chromosomal phylogeny reported here, allow the identification of several whole plasmid transfer events among these species. Phylogenetic analyses of the plasmid partition genes show that a majority of the plasmid compatibility types arose early, most likely before separation of the Lyme agent Borreliella and relapsing fever Borrelia clades, and this, with occasional cross species plasmid transfers, has resulted in few if any species-specific or geographic region-specific Borreliella plasmid types. Conclusions: The primordial origin and persistent maintenance of the Borreliella plasmid types support their functional indispensability as well as evolutionary roles in facilitating genome diversity. The improved resolution of Borreliella plasmid phylogeny based on conserved partition-gene clusters will lead to better determination of gene orthology which is essential for prediction of biological function, and it will provide a basis for inferring detailed evolutionary mechanisms of Borreliella genomic variability including homologous gene and plasmid exchanges as well as nonhomologous rearrangements

Phylogenomic Identification of Regulatory Sequences in Bacteria: an Analysis of Statistical Power and an Application to Borrelia burgdorferi Sensu Lato

Phylogenomic footprinting is an approach for ab initio identification of genome-wide regulatory elements in bacterial species based on sequence conservation. The statistical power of the phylogenomic approach depends on the degree of sequence conservation, the length of regulatory elements, and the level of phylogenetic divergence among genomes. Building on an earlier model, we propose a binomial model that uses synonymous tree lengths as neutral expectations for determining the statistical significance of conserved intergenic spacer (IGS) sequences. Simulations show that the binomial model is robust to variations in the value of evolutionary parameters, including base frequencies and the transition-to-transversion ratio. We used the model to search for regulatory sequences in the Lyme disease species group (Borrelia burgdorferi sensu lato) using 23 genomes. The model indicates that the currently available set of Borrelia genomes would not yield regulatory sequences shorter than five bases, suggesting that genome sequences of additional B. burgdorferi sensu lato species are needed. Nevertheless, we show that previously known regulatory elements are indeed strongly conserved in sequence or structure across these Borrelia species. Further, we predict with sufficient confidence two new RpoS binding sites, 39 promoters, 19 transcription terminators, 28 noncoding RNAs, and four sets of coregulated genes. These putative cis- and trans-regulatory elements suggest novel, Borrelia-specific mechanisms regulating the transition between the tick and host environments, a key adaptation and virulence mechanism of B. burgdorferi. Alignments of IGS sequences are available on BorreliaBase.org, an online database of orthologous open reading frame (ORF) and IGS sequences in Borrelia

BorreliaBase: a phylogeny-centered browser of Borrelia genomes

Background The bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever. The number of publicly available Borrelia genomic sequences is growing rapidly with the discovery and sequencing of Borrelia strains worldwide. There is however a lack of dedicated online databases to facilitate comparative analyses of Borrelia genomes. Description We have developed BorreliaBase, an online database for comparative browsing of Borrelia genomes. The database is currently populated with sequences from 35 genomes of eight Lyme-borreliosis (LB) group Borrelia species and 7 Relapsing-fever (RF) group Borrelia species. Distinct from genome repositories and aggregator databases, BorreliaBase serves manually curated comparative-genomic data including genome-based phylogeny, genome synteny, and sequence alignments of orthologous genes and intergenic spacers. Conclusions With a genome phylogeny at its center, BorreliaBase allows online identification of hypervariable lipoprotein genes, potential regulatory elements, and recombination footprints by providing evolution-based expectations of sequence variability at each genomic locus. The phylo-centric design of BorreliaBase (http://borreliabase.org) is a novel model for interactive browsing and comparative analysis of bacterial genomes online

Genomic Insights into Mechanisms of Microbial Evolution and Evolution-inspired Strategies to Combat Pathogen Diversity

We live in an era of emerging infectious diseases that are increasingly common, rapidly spreading, and gravely devastating. Lyme disease, caused by bacteria belonging to the genus Borreliella, is rapidly rising in the Northern Hemisphere because of geographic range expansion of both the tick vectors and the pathogens. Evolutionary comparative analysis of Borreliella genomes is a key to understanding the phylogeographic history and mechanisms of their global diversification. Moreover, genomic variations in Borreliella associated with human pathogenicity, e.g., at loci encoding cell-surface antigens interacting with the vertebrate hosts, have not been fully identified. Similarly, the ongoing COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is bringing unprecedented loss of human lives and turmoil in global economic and social orders. While the genome of SARS-CoV-2 coronavirus causing the COVID-19 pandemic is rapidly evolving during the global pandemic, it is not clear how to distinguish the most consequential mutations, such as those associated with human virulence and immune escape, among the numerous genomic changes elsewhere. By analyzing the genomic sequences of microbial pathogens in an evolutionary framework, I reconstructed biogeographic histories of Lyme disease pathogens. My studies identified that evolutionary mechanisms of SARS-CoV-2 genome diversification driven by natural selection including escape from host immunity. I also implemented novel evolution-informed strategies to combat pathogen diversification. In chapter 1, I report forty-four newly completed genomes of nineteen Borreliella species from across the world, a comprehensive biogeographic history of their global diversification, and a highly dynamic and fluid plasmid composition and structure mediated by rapid gene duplication, losses, and translocation. In chapter 2, I show that Lyme disease-causing bacterium Borreliella burgdorferi produces an outer surface protein C (OspC) that displays high antigenicity specificity. To overcome the challenge of OspC antigenic diversity in the development of preventive clinical vaccine strategies, I report evolution-inspired designs of synthetic antigens that are more broadly reactive than the natural OspC variants. These synthetic evolutionary analogs of OspC showed promise as diagnostic and vaccine candidates against diverse pathogen strains coexisting in the endemic areas of Lyme disease in the United States. Our automated evolution-based computational design opens a novel path to combating other fast-evolving microbial pathogens as well. In chapter 3, I report an evolutionary analysis of close to one million SARS-CoV-2 genomes and show that a key signature of human-adaptive mutations is their tendency to form clusters of shared allelic frequency trajectories over time. Furthermore, my colleagues and I have developed novel software tools including a database, a bioinformatics pipeline, a genome-evolution simulator, and a web interface to facilitate rapid identification of genomic signatures of viral adaptation to humans during the current and future viral outbreaks. In combination, these chapters offer a comprehensive understanding of key drivers of adaptive genome evolution of two major microbial pathogens, provide a set of software tools and pipelines for analyzing microbial genome variability, and propose an evolution-based strategy to combat pathogen diversification

Primordial origin and diversification of plasmids in Lyme disease agent bacteria

Abstract Background With approximately one-third of their genomes consisting of linear and circular plasmids, the Lyme disease agent cluster of species has the most complex genomes among known bacteria. We report here a comparative analysis of plasmids in eleven Borreliella (also known as Borrelia burgdorferi sensu lato) species. Results We sequenced the complete genomes of two B. afzelii, two B. garinii, and individual B. spielmanii, B. bissettiae, B. valaisiana and B. finlandensis isolates. These individual isolates carry between seven and sixteen plasmids, and together harbor 99 plasmids. We report here a comparative analysis of these plasmids, along with 70 additional Borreliella plasmids available in the public sequence databases. We identify only one new putative plasmid compatibility type (the 30th) among these 169 plasmid sequences, suggesting that all or nearly all such types have now been discovered. We find that the linear plasmids in the non-B. burgdorferi species have undergone the same kinds of apparently random, chaotic rearrangements mediated by non-homologous recombination that we previously discovered in B. burgdorferi. These rearrangements occurred independently in the different species lineages, and they, along with an expanded chromosomal phylogeny reported here, allow the identification of several whole plasmid transfer events among these species. Phylogenetic analyses of the plasmid partition genes show that a majority of the plasmid compatibility types arose early, most likely before separation of the Lyme agent Borreliella and relapsing fever Borrelia clades, and this, with occasional cross species plasmid transfers, has resulted in few if any species-specific or geographic region-specific Borreliella plasmid types. Conclusions The primordial origin and persistent maintenance of the Borreliella plasmid types support their functional indispensability as well as evolutionary roles in facilitating genome diversity. The improved resolution of Borreliella plasmid phylogeny based on conserved partition-gene clusters will lead to better determination of gene orthology which is essential for prediction of biological function, and it will provide a basis for inferring detailed evolutionary mechanisms of Borreliella genomic variability including homologous gene and plasmid exchanges as well as non-homologous rearrangements

BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines

Abstract Background Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl (http://bioperl.org) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users. Results Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of the most popular BioPerl modules readily accessible on the command line to novice as well as to experienced bioinformatics practitioners. The initial release of BpWrapper includes four utilities with concise command-line user interfaces, bioseq, bioaln, biotree, and biopop, specialized for manipulation of molecular sequences, sequence alignments, phylogenetic trees, and DNA polymorphisms, respectively. Over a hundred methods are currently available as command-line options and new methods are easily incorporated. Performance of BpWrapper utilities lags that of precompiled utilities while equivalent to that of other utilities based on BioPerl. BpWrapper has been tested on BioPerl Release 1.6, Perl versions 5.10.1 to 5.25.10, and operating systems including Apple macOS, Microsoft Windows, and GNU/Linux. Release code is available from the Comprehensive Perl Archive Network (CPAN) at https://metacpan.org/pod/Bio::BPWrapper. Source code is available on GitHub at https://github.com/bioperl/p5-bpwrapper. Conclusions BpWrapper improves on existing sequence utilities by following the design principles of Unix text utilities such including a concise user interface, extensive command-line options, and standard input/output for serialized operations. Further, dozens of novel methods for manipulation of sequences, alignments, and phylogenetic trees, unavailable in existing utilities (e.g., EMBOSS, Newick Utilities, and FAST), are provided. Bioinformaticians should find BpWrapper useful for rapid prototyping of workflows on the command-line without creating custom scripts for comparative genomics and other bioinformatics applications

Additional file 1: of Primordial origin and diversification of plasmids in Lyme disease agent bacteria

Figure S1. Borreliella plasmid PFam32 protein neighbor-joining tree. Figure S2. Two examples of Borreliella linear plasmids with low protein coding potential. Figure S3. Comparative maps of linear plasmids in Borreliella isolates. Maps of the following linear plasmids are shown in the following panels: A, lp5; B, lp17; C, lp25; D, lp28–2, lp28–6, lp28–7 and lp28–9; E, lp28–3; F, VS116 lp28–3; G, lp28–4; H, lp28–8; I, lp32; J, lp36; K, lp38; L, lp56. Figure S4. The PFam54 gene cluster of the Borreliella lp54 plasmids. Figure S5. Ends of the Borreliella linear chromosome sequences. Figure S6. Comparative maps of cp9 plasmids in Borreliella isolates. Figure S7. Orphan cp32-like contigs in the B. spielmanii A14S genome. Figure S8. Rearrangements in cp32-like plasmids in NBu-Borreliella genomes. Figure S9. B. bissettiae DN127 66 kbp circular plasmid cp32-quad. Figure S10. B. finlandensis SV1 integration of cp32 into lp54. Figure S11. Borreliella and relapsing fever Borrelia PFam32 neighbor-joining tree. Table S1. Borreliella and relapsing fever Borrelia PFam32. (PDF 6030 kb

Additional file 1: of BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines

A reference card for the four BpWrapper utilities (PDF 758 kb