VIRTIGATION partner EMWEB has introduced key improvements to its Genome Detective tool to enhance the detection of plant viruses.
Article by Tiziana Centofanti from the VIRTIGATION project
Genome Detective: An online tool for virus epidemiology
Scientists trying to track emerging plant viruses in tomatoes and cucurbits can use the Genome Detective tool to examine the RNA and DNA of these viruses. This software developed by VIRTIGATION partner EMWEB helps them to quickly and accurately read the genetic code of a plant virus, which is like its instruction manual. To better accommodate the collection and analysis of plant virus samples, especially in the context of metagenomic viral sequences and epidemiological metadata for plant virus outbreak analysis as those performed in VIRTIGATION, EMWEB recently implemented two key improvements to the Genome Detective tool. Moreover, for the ToBRFV plant virus, EMWEB has released the ToBRFV typing tool. This tool uses Blast and phylogenetic methods in order to identify the ToBRFV clade of a nucleotide sequence.
Extensive metadata on plant virus samples
The Genome Detective tool can store and organize key information about each virus sample, as e.g. where it was found or what type of plant it infected. This metadata is crucial for understanding the context of viral outbreaks, and enables tracking of factors as e.g. host properties, environmental conditions, and co-infections. Users can directly enter the information into the software or upload it from a spreadsheet, making it easy to keep track of many samples at once. This functionality supports various data entry methods, including text-based and coordinate-based geolocation, as well as different descriptor types like free text fields, checkboxes, and dropdown menus. The Genome Detective tool helps to check for mistakes in the information to make sure everything is accurate. This helps scientists understand how plant viruses are spreading and what factors might be contributing to their outbreaks. Users can also easily search for samples based on these clues.
Ability to read long virus DNA and RNA
VIRTIGATION scientists have developed a new lab technique that creates very long pieces of virus DNA that are easier to read with certain machines (i.e. new Rolling Circle Amplification (RCA) – a method used to amplify circular DNA molecules – wet-lab protocol with Oxford Nanopore Technologies (ONT) sequencing). This novel protocol produces long reads containing multiple copies of a circular viral genome. The Genome Detective software can now handle this type of data, i.e. enabling scientists to access a new magnifying glass to see finer details. This new method creates many copies of the virus’s genetic material, which can introduce errors. The integrated pipeline addresses the challenges associated with analyzing this type of data, specifically within-read errors and the need to identify multiple viral variants within a single sample. The circular nature of some viral genomes (like begomoviruses) and the high error rate of ONT reads pose thereby key challenges.
The Genome Detective tool now has built-in tools to correct these errors by linearizing and rotating the circular reads, to align them with a reference genome and then performing multiple sequence alignment. By using a statistical approach with binomial distribution, coverage depth, and the expected error rate for ONT data, sequencing errors can be identified and corrected, resulting in more accurate reads and improved resolution for variant detection. This new improvement helps to identify different versions of the same virus within a single plant, which helps understand how the virus is changing and adapting.
Multiple benefits for plant scientists and users
Thanks to these improvements, plant scientists and users can benefit in multiple ways from the Genome Detective software:
- Track outbreaks: By combining the genetic information of the virus with the extra details (the “clues”), they can better understand how plant viruses are spreading and identify the source of outbreaks.
- Find different virus types: The new Genome Detective functionalities can find even small differences between viruses, helping e.g. plant scientists understand how they are evolving and if they are becoming more dangerous to plants.
- Fight plant virus diseases: By understanding the viruses better, scientists, the agro-industry and other value chain actors can develop better ways to protect tomato and cucurbits plants.
EMWEB’s improvements have already been successfully applied to analyze viral sequences from Solanaceae (tomato) and Cucurbitaceae (cucurbit) plants infected with various viruses, including begomoviruses like Tomato yellow leaf curl Sardinia virus (TYLCSV) and ToLCNDV, as well as the ToBRFV tobamovirus. The Genome Detective tool has thereby proven to be effective in resolving complex intraplant viral populations and mixed infections of closely related isolates.
Read here the deliverable “Genome Detective Platform adaptations for plant viruses” produced by VIRTIGATION partner EMWEB, which describes the improvements made in more detail.
Watch also here EMWEB lead scientist Sam Dierickx describe the advantages of the Genome Detective software in our VIRTIGATION “Research in Brief” video series.
© Title image: EMWEB
