WASPS: web-assisted symbolic plasmid synteny server

VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes

MOTIVATION

Studying the genetic makeup of viruses and phages through genome analysis is crucial for comprehending their function in causing diseases, progressing medicine, tracing their evolutionary history, monitoring the environment, and creating innovative biotechnologies. However, accessing the necessary data can be challenging due to a lack of dedicated comparative genomic tools and viral and phage databases, which are often outdated. Moreover, many wet bench experimentalists may not have the computational proficiency required to manipulate large amounts of genomic data.

RESULTS

We have developed VAPEX (Virus And Phage EXplorer), a web server which is supported by a database and features a user-friendly web interface. This tool enables users to easily perform various genomic analysis queries on all natural viruses and phages that have been fully sequenced and are listed in the NCBI compendium. VAPEX therefore excels in producing visual depictions of fully resolved synteny maps, which is one of its key strengths. VAPEX has the ability to exhibit a vast array of orthologous gene classes simultaneously through the use of symbolic representation. Additionally, VAPEX can fully analyze user-submitted viral and phage genomes, including those that have not yet been annotated.

AVAILABILITY AND IMPLEMENTATION

VAPEX can be accessed from all current web browsers such as Chrome, Firefox, Edge, Safari, and Opera. VAPEX is freely accessible at https://archaea.i2bc.paris-saclay.fr/vapex/.

Epitopes screening and vaccine molecular design of SADS-CoV based on immunoinformatics

The regional outbreak of the Swine acute diarrhea syndrome coronavirus (SADS-CoV) has seriously threatened the swine industry. There is an urgent need to discover safe and effective vaccines to contain them quickly. The coronavirus spike protein mediates virus entry into host cells, one of the most important antigenic determinants and a potential vaccine target. Therefore, this study aims to conduct a predictive analysis of the epitope of S protein B cells and T cells (MHC class I and class II) by immunoinformatics methods by screening and identifying protective antigenic epitopes that induce major neutralized antibodies and activate immune responses to construct epitope vaccines. The study explored primary, secondary, and tertiary structures, disulfide bonds, protein docking, immune response simulation, and seamless cloning of epitope vaccines. The results show that the spike protein dominant epitope of the screening has a high conservativeness and coverage of IFN-γ, IL-4-positive Th epitope, and CTL epitope. The constructed epitope vaccine interacts stably with TLR-3 receptors, and the immune response simulation shows good immunogenicity, which could effectively activate humoral and cellular immunity. After codon optimization, it was highly likely to be efficiently and stably expressed in the Escherichia coli K12 expression system. Therefore, the constructed epitope vaccine will provide a new theoretical basis for the design of SADS-CoV antiviral drugs and related research on coronaviruses such as SARS-CoV-2.

Exploring short k-mer profiles in cells and mobile elements from Archaea highlights the major influence of both the ecological niche and evolutionary history

BACKGROUND

K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors.

RESULTS

For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile.

CONCLUSION

This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.