VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data
NIKOLSKI, Macha
Institut de biochimie et génétique cellulaires [IBGC]
Centre de Bioinformatique de Bordeaux [CBIB]
< Reduce
Institut de biochimie et génétique cellulaires [IBGC]
Centre de Bioinformatique de Bordeaux [CBIB]
Language
en
Article de revue
This item was published in
Frontiers in Bioinformatics. 2022-05-13, vol. 2, p. 867111
Frontiers Media
English Abstract
High-throughput sequencing has provided the capacity of broad virus detection for both known and unknown viruses in a variety of hosts and habitats. It has been successfully applied for novel virus discovery in many ...Read more >
High-throughput sequencing has provided the capacity of broad virus detection for both known and unknown viruses in a variety of hosts and habitats. It has been successfully applied for novel virus discovery in many agricultural crops, leading to the current drive to apply this technology routinely for plant health diagnostics. For this, efficient and precise methods for sequencing-based virus detection and discovery are essential. However, both existing alignment-based methods relying on reference databases and even more recent machine learning approaches are not efficient enough in detecting unknown viruses in RNAseq datasets of plant viromes. We present VirHunter, a deep learning convolutional neural network approach, to detect novel and known viruses in assemblies of sequencing datasets. While our method is generally applicable to a variety of viruses, here, we trained and evaluated it specifically for RNA viruses by reinforcing the coding sequences’ content in the training dataset. Trained on the NCBI plant viruses data for three different host species (peach, grapevine, and sugar beet), VirHunter outperformed the state-of-the-art method, DeepVirFinder, for the detection of novel viruses, both in the synthetic leave-out setting and on the 12 newly acquired RNAseq datasets. Compared with the traditional tBLASTx approach, VirHunter has consistently exhibited better results in the majority of leave-out experiments. In conclusion, we have shown that VirHunter can be used to streamline the analyses of plant HTS-acquired viromes and is particularly well suited for the detection of novel viral contigs, in RNAseq datasets.Read less <
English Keywords
novel virus detection
RNA viruses
plant virome
alignment-free method
deep learning
artificial neural network
Origin
Hal importedCollections