Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing

Abstract Next-generation sequencing is a robust approach to sequence plant virus genomes in a very short amount of time compared to traditional sequencing methods. Maize dwarf mosaic virus (MDMV) is one of the most important plant viruses worldwide and a significant threat to maize production. In th...

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Autores principales:	Dulanjani Wijayasekara, Akhtar Ali
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/05d3dc5b70c0497cb8a932aa4ba71001
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spelling	oai:doaj.org-article:05d3dc5b70c0497cb8a932aa4ba710012021-12-02T17:27:11ZEvolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing10.1038/s41598-021-98299-92045-2322https://doaj.org/article/05d3dc5b70c0497cb8a932aa4ba710012021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98299-9https://doaj.org/toc/2045-2322Abstract Next-generation sequencing is a robust approach to sequence plant virus genomes in a very short amount of time compared to traditional sequencing methods. Maize dwarf mosaic virus (MDMV) is one of the most important plant viruses worldwide and a significant threat to maize production. In this study, we sequenced 19 MDMV isolates (10 from Johnsongrass and 9 from maize) collected in Oklahoma and Missouri during 2017–2019 using Illumina sequencing and determined the genetic diversity. Sequence reads were assembled and 19 nearly complete genome sequences of MDMV isolates were obtained. Phylogenetic analysis based on complete genomes nucleotide and amino acid sequences revealed two main clusters and a close evolutionary relationship among 19 MDMV isolates. Statistical analysis of individual genes for site-specific selection revealed that all genes are under negative selection. The fixation index (FST) analysis of the MDMV isolates revealed no gene flow between the two main phylogenetic clusters, which emphasizes the divergence of MDMV isolates from the USA. Among the USA MDMV isolates, the mean genetic distance (d) and nucleotide diversity ((π) were highest in the P1 gene coding region. This is the first detailed study on the evolutionary relationship of MDMV isolates based on the nearly complete genome analysis from maize and Johnsongrass.Dulanjani WijayasekaraAkhtar AliNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dulanjani Wijayasekara Akhtar Ali Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing
description	Abstract Next-generation sequencing is a robust approach to sequence plant virus genomes in a very short amount of time compared to traditional sequencing methods. Maize dwarf mosaic virus (MDMV) is one of the most important plant viruses worldwide and a significant threat to maize production. In this study, we sequenced 19 MDMV isolates (10 from Johnsongrass and 9 from maize) collected in Oklahoma and Missouri during 2017–2019 using Illumina sequencing and determined the genetic diversity. Sequence reads were assembled and 19 nearly complete genome sequences of MDMV isolates were obtained. Phylogenetic analysis based on complete genomes nucleotide and amino acid sequences revealed two main clusters and a close evolutionary relationship among 19 MDMV isolates. Statistical analysis of individual genes for site-specific selection revealed that all genes are under negative selection. The fixation index (FST) analysis of the MDMV isolates revealed no gene flow between the two main phylogenetic clusters, which emphasizes the divergence of MDMV isolates from the USA. Among the USA MDMV isolates, the mean genetic distance (d) and nucleotide diversity ((π) were highest in the P1 gene coding region. This is the first detailed study on the evolutionary relationship of MDMV isolates based on the nearly complete genome analysis from maize and Johnsongrass.
format	article
author	Dulanjani Wijayasekara Akhtar Ali
author_facet	Dulanjani Wijayasekara Akhtar Ali
author_sort	Dulanjani Wijayasekara
title	Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing
title_short	Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing
title_full	Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing
title_fullStr	Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing
title_full_unstemmed	Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing
title_sort	evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/05d3dc5b70c0497cb8a932aa4ba71001
work_keys_str_mv	AT dulanjaniwijayasekara evolutionarystudyofmaizedwarfmosaicvirususingnearlycompletegenomesequencesacquiredbynextgenerationsequencing AT akhtarali evolutionarystudyofmaizedwarfmosaicvirususingnearlycompletegenomesequencesacquiredbynextgenerationsequencing
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Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing

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