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Virology Journal
Published in: Virology Journal 1/2023

Open Access 01-12-2023 | Research

MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus

Authors: Karthic Krishnan, Vinaya Kumar Katneni, Sudheesh K. Prabhudas, Nimisha Kaikkolante, Ashok Kumar Jangam, Upendra Kumar Katneni, Chris Hauton, Luca Peruzza, Shashi Shekhar Mudagandur, Vijayan K. Koyadan, Jithendran Karingalakkandy Poochirian, Joykrushna Jena

Published in: Virology Journal | Issue 1/2023

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Abstract

Background

The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature.

Methods

We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes.

Results

We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases.

Conclusions

Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.
Appendix
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Metadata
Title
MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
Authors
Karthic Krishnan
Vinaya Kumar Katneni
Sudheesh K. Prabhudas
Nimisha Kaikkolante
Ashok Kumar Jangam
Upendra Kumar Katneni
Chris Hauton
Luca Peruzza
Shashi Shekhar Mudagandur
Vijayan K. Koyadan
Jithendran Karingalakkandy Poochirian
Joykrushna Jena
Publication date
01-12-2023
Publisher
BioMed Central
Published in
Virology Journal / Issue 1/2023
Electronic ISSN: 1743-422X
DOI
https://doi.org/10.1186/s12985-023-02035-w

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