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

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 nomen...

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Autores principales: Krishnan, Karthic, Katneni, Vinaya Kumar, Prabhudas, Sudheesh K., Kaikkolante, Nimisha, Jangam, Ashok Kumar, Katneni, Upendra Kumar, Hauton, Chris, Peruzza, Luca, Mudagandur, Shashi Shekhar, Koyadan, Vijayan K., Poochirian, Jithendran Karingalakkandy, Jena, Joykrushna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10111743/
https://www.ncbi.nlm.nih.gov/pubmed/37072853
http://dx.doi.org/10.1186/s12985-023-02035-w
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author Krishnan, Karthic
Katneni, Vinaya Kumar
Prabhudas, Sudheesh K.
Kaikkolante, Nimisha
Jangam, Ashok Kumar
Katneni, Upendra Kumar
Hauton, Chris
Peruzza, Luca
Mudagandur, Shashi Shekhar
Koyadan, Vijayan K.
Poochirian, Jithendran Karingalakkandy
Jena, Joykrushna
author_facet Krishnan, Karthic
Katneni, Vinaya Kumar
Prabhudas, Sudheesh K.
Kaikkolante, Nimisha
Jangam, Ashok Kumar
Katneni, Upendra Kumar
Hauton, Chris
Peruzza, Luca
Mudagandur, Shashi Shekhar
Koyadan, Vijayan K.
Poochirian, Jithendran Karingalakkandy
Jena, Joykrushna
author_sort Krishnan, Karthic
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-023-02035-w.
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spelling pubmed-101117432023-04-19 MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus Krishnan, Karthic Katneni, Vinaya Kumar Prabhudas, Sudheesh K. Kaikkolante, Nimisha Jangam, Ashok Kumar Katneni, Upendra Kumar Hauton, Chris Peruzza, Luca Mudagandur, Shashi Shekhar Koyadan, Vijayan K. Poochirian, Jithendran Karingalakkandy Jena, Joykrushna Virol J Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-023-02035-w. BioMed Central 2023-04-18 /pmc/articles/PMC10111743/ /pubmed/37072853 http://dx.doi.org/10.1186/s12985-023-02035-w Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Krishnan, Karthic
Katneni, Vinaya Kumar
Prabhudas, Sudheesh K.
Kaikkolante, Nimisha
Jangam, Ashok Kumar
Katneni, Upendra Kumar
Hauton, Chris
Peruzza, Luca
Mudagandur, Shashi Shekhar
Koyadan, Vijayan K.
Poochirian, Jithendran Karingalakkandy
Jena, Joykrushna
MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
title MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
title_full MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
title_fullStr MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
title_full_unstemmed MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
title_short MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus
title_sort mrf: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal dna virus
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10111743/
https://www.ncbi.nlm.nih.gov/pubmed/37072853
http://dx.doi.org/10.1186/s12985-023-02035-w
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