On K-peptide length in composition vector phylogeny of prokaryotes

Development of an Online Genome Sequence Comparison Resource for Bacillus cereus sensu lato Strains Using the Efficient Composition Vector Method

An automated method was developed for differentiating closely related B. cereus sensu lato (s.l.) species, especially biopesticide Bacillus thuringiensis, from other human pathogens, B. anthracis and B. cereus sensu stricto (s.s.). In the current research, four typing methods were initially compared, including multi-locus sequence typing (MLST), single-copy core genes phylogenetic analysis (SCCGPA), dispensable genes content pattern analysis (DGCPA) and composition vector tree (CVTree), to analyze the genomic variability of 23 B. thuringiensis strains from aizawai, kurstaki, israelensis, thuringiensis and morrisoni serovars. The CVTree method was the best option to be used for typing B. thuringiensis strains since it proved to be the fastest method, whilst giving high-resolution data about the strains. In addition, CVTree agrees well with ANI-based method, revealing the relationship between B. thuringiensis and other B. cereus s.l. species. Based on these data, an online genome sequence comparison resource was built for Bacillus strains called the Bacillus Typing Bioinformatics Database to facilitate strain identification and characterization.

Quercetin mitigates rheumatoid arthritis by inhibiting adenosine deaminase in rats

Rheumatoid arthritis (RA) is a chronic inflammatory joint disease characterized by synovial proliferation and bone destruction. Adenosine deaminase (ADA) is a key inflammatory enzyme that increases joint stiffness and pain in RA. In this study, we evaluated the in-silico, and in vivo inhibitory effect of quercetin isolated from Egyptian Fenugreek on ADA enzyme activity. We also determined the combinatorial effect of quercetin on methotrexate mediated anti-inflammatory efficacy and toxicity. In-silico molecular docking was conducted and confirmed in an in vivo RA rat model. The results showed that the inhibition constant of quercetin on joint ADA by docking and in-vitro was 61.9 and 55.5 mM, respectively. Therefore, quercetin exhibits anti-inflammatory effect in a rat RA model as evidenced by reducing the specific activity of ADA in joint tissues, lower jaw volume, enhance body weight, downregulate ADA gene expression, reduce levels of RA cytokines interleukin-1^β, interleukin-6, tumor necrosis factor-α, also, rheumatoid factor, C-reactive protein, and anti-cyclic citrullinated peptide RA biomarker levels. These findings demonstrate that the purified quercetin has a promising anti-inflammatory effect against RA disease through its inhibitory effects on the ADA enzyme. Furthermore, isolated quercetin improved the anti-inflammatory efficacy of methotrexate, reduced its toxic effects by increasing antioxidant enzymes and reducing oxidative stress.

CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool based on Composition Vectors of Genomes

CVTree is an alignment-free algorithm to infer phylogenetic relationships from genome sequences. It had been successfully applied to study phylogeny and taxonomy of viruses, prokaryotes, and fungi based on the whole genomes, as well as chloroplasts, mitochondria, and metagenomes. Here we presented the standalone software for the CVTree algorithm. In the software, an extensible parallel workflow for the CVTree algorithm was designed. Based on the workflow, new alignment-free methods were also implemented. And by examining the phylogeny and taxonomy of 13,903 prokaryotes based on 16S rRNA sequences, we showed that CVTree software is an efficient and effective tool for the studying of phylogeny and taxonomy based on genome sequences. Code availability: https://github.com/ghzuo/cvtree.

Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants

Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of cultured members is low. Here we report four cultivated Verrucomicrobia isolated from rice, putatively representing four novel species, and a novel subdivision. The aerobic strains were isolated from roots or rhizomes of Oryza sativa and O. longistaminata. Two of them are the first cultivated endophytes of Verrucomicrobia, as validated by confocal laser scanning microscopy inside rice roots after re-infection under sterile conditions. This extended known verrucomicrobial niche spaces. Two strains were promoting root growth of rice. Discovery of root compartment-specific Verrucomicrobia permitted an across-phylum comparison of the genomic conformance to life in soil, rhizoplane or inside roots. Genome-wide protein domain comparison with niche-specific reference bacteria from distant phyla revealed signature protein domains which differentiated lifestyles in these microhabitats. Our study enabled us to shed light into the dark microbial matter of root Verrucomicrobia, to define genetic drivers for niche adaptation of bacteria to plant roots, and provides cultured strains for revealing causal relationships in plant-microbe interactions by reductionist approaches.

Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome

The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.

On monospecific genera in prokaryotic taxonomy

A monospecific genus contains a single species ever since it was proposed. Though formally more than half of the known prokaryotic genera are monospecific, we pick up those which actually raise taxonomic problems by violating monophyly of the taxon within which it resides. Taking monophyly as a guiding principle, our arguments are based on simultaneous support from 16S rRNA sequence analysis and whole-genome phylogeny of prokaryotes, as provided by the LVTree Viewer and CVTree Web Server, respectively. The main purpose of this study consists in calling attention to this specific way of global taxonomic analysis. Therefore, we refrain from making formal emendations for the time being.

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species

The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories, model organisms, and human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus, and A. steynii) have been whole-genome PacBio sequenced to provide genetic references in three Aspergillus sections. A. taichungensis and A. candidus also were sequenced for SM elucidation. Thirteen Aspergillus genomes were analyzed with comparative genomics to determine phylogeny and genetic diversity, showing that each presented genome contains 15-27% genes not found in other sequenced Aspergilli. In particular, A. novofumigatus was compared with the pathogenic species A. fumigatus This suggests that A. novofumigatus can produce most of the same allergens, virulence, and pathogenicity factors as A. fumigatus, suggesting that A. novofumigatus could be as pathogenic as A. fumigatus Furthermore, SMs were linked to gene clusters based on biological and chemical knowledge and analysis, genome sequences, and predictive algorithms. We thus identify putative SM clusters for aflatoxin, chlorflavonin, and ochrindol in A. ochraceoroseus, A. campestris, and A. steynii, respectively, and novofumigatonin, ent-cycloechinulin, and epi-aszonalenins in A. novofumigatus Our study delivers six fungal genomes, showing the large diversity found in the Aspergillus genus; highlights the potential for discovery of beneficial or harmful SMs; and supports reports of A. novofumigatus pathogenicity. It also shows how biological, biochemical, and genomic information can be combined to identify genes involved in the biosynthesis of specific SMs.

Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom

Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method. Six methods have seen extensive use in previous fungal studies, while a Bayesian supertree method is novel to fungal phylogenomics. We find that both established and novel phylogenomic methods can accurately reconstruct the fungal kingdom. Finally, we discuss the accuracy and suitability of each phylogenomic method utilized.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis

A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey's Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.