Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies

High-throughput sequencing from symptomatic tomato and pepper plants collected in Panama rendered the complete genome of the southern tomato virus (isolate STV_Panama) and bell pepper endornavirus (isolate BPEV_Panama), and almost-complete genomes of three other BPEV isolates. Tomato chlorosis virus...

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Autores principales:	Luis Galipienso, Laura Elvira-González, Leonardo Velasco, José Ángel Herrera-Vásquez, Luis Rubio
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	high throughput sequencing STV BPEV pepper tomato nucleotide diversity Botany QK1-989
Acceso en línea:	https://doaj.org/article/d8a42fffb4d74def9fc8459b1b5c9876
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spelling	oai:doaj.org-article:d8a42fffb4d74def9fc8459b1b5c98762021-11-25T18:44:56ZDetection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies10.3390/plants101122952223-7747https://doaj.org/article/d8a42fffb4d74def9fc8459b1b5c98762021-10-01T00:00:00Zhttps://www.mdpi.com/2223-7747/10/11/2295https://doaj.org/toc/2223-7747High-throughput sequencing from symptomatic tomato and pepper plants collected in Panama rendered the complete genome of the southern tomato virus (isolate STV_Panama) and bell pepper endornavirus (isolate BPEV_Panama), and almost-complete genomes of three other BPEV isolates. Tomato chlorosis virus, tomato mosaic virus, and impatiens necrotic spot virus were also detected. Analysis of the complete genome of STV and BPEV worldwide isolates revealed nucleotide diversities of 0.004246 and 0.070523, respectively. Bayesian phylogenetic analysis showed two main groups for each virus (I and II), and several subgroups for BPEV (IA, IB, IC, IIA and IIB). Isolate STV_Panama clustered with NC_12-03-08 from USA and Tom3-T from France (99.97% nucleotide identity) in Group I and BPEV_Panama was close to the Canadian isolate BPEV_Ontario (99.66% nucleotide identity) in Subgroup IB. No correlation was observed between geographic and genetic distances for both viruses. Panamanian BPEV isolates were divergent, belonging to Groups I and II (nucleotide identities > 87.33%). Evolutionary analysis showed purifying selection in all encoding regions of both viruses, being stronger in the overlapping region of both STV genes. Finally, recombination was detected in BPEV but not in STV. This is the first report of STV and BPEV in Panama.Luis GalipiensoLaura Elvira-GonzálezLeonardo VelascoJosé Ángel Herrera-VásquezLuis RubioMDPI AGarticlehigh throughput sequencingSTVBPEVpeppertomatonucleotide diversityBotanyQK1-989ENPlants, Vol 10, Iss 2295, p 2295 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	high throughput sequencing STV BPEV pepper tomato nucleotide diversity Botany QK1-989
spellingShingle	high throughput sequencing STV BPEV pepper tomato nucleotide diversity Botany QK1-989 Luis Galipienso Laura Elvira-González Leonardo Velasco José Ángel Herrera-Vásquez Luis Rubio Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies
description	High-throughput sequencing from symptomatic tomato and pepper plants collected in Panama rendered the complete genome of the southern tomato virus (isolate STV_Panama) and bell pepper endornavirus (isolate BPEV_Panama), and almost-complete genomes of three other BPEV isolates. Tomato chlorosis virus, tomato mosaic virus, and impatiens necrotic spot virus were also detected. Analysis of the complete genome of STV and BPEV worldwide isolates revealed nucleotide diversities of 0.004246 and 0.070523, respectively. Bayesian phylogenetic analysis showed two main groups for each virus (I and II), and several subgroups for BPEV (IA, IB, IC, IIA and IIB). Isolate STV_Panama clustered with NC_12-03-08 from USA and Tom3-T from France (99.97% nucleotide identity) in Group I and BPEV_Panama was close to the Canadian isolate BPEV_Ontario (99.66% nucleotide identity) in Subgroup IB. No correlation was observed between geographic and genetic distances for both viruses. Panamanian BPEV isolates were divergent, belonging to Groups I and II (nucleotide identities > 87.33%). Evolutionary analysis showed purifying selection in all encoding regions of both viruses, being stronger in the overlapping region of both STV genes. Finally, recombination was detected in BPEV but not in STV. This is the first report of STV and BPEV in Panama.
format	article
author	Luis Galipienso Laura Elvira-González Leonardo Velasco José Ángel Herrera-Vásquez Luis Rubio
author_facet	Luis Galipienso Laura Elvira-González Leonardo Velasco José Ángel Herrera-Vásquez Luis Rubio
author_sort	Luis Galipienso
title	Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies
title_short	Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies
title_full	Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies
title_fullStr	Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies
title_full_unstemmed	Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies
title_sort	detection of persistent viruses by high-throughput sequencing in tomato and pepper from panama: phylogenetic and evolutionary studies
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/d8a42fffb4d74def9fc8459b1b5c9876
work_keys_str_mv	AT luisgalipienso detectionofpersistentvirusesbyhighthroughputsequencingintomatoandpepperfrompanamaphylogeneticandevolutionarystudies AT lauraelviragonzalez detectionofpersistentvirusesbyhighthroughputsequencingintomatoandpepperfrompanamaphylogeneticandevolutionarystudies AT leonardovelasco detectionofpersistentvirusesbyhighthroughputsequencingintomatoandpepperfrompanamaphylogeneticandevolutionarystudies AT joseangelherreravasquez detectionofpersistentvirusesbyhighthroughputsequencingintomatoandpepperfrompanamaphylogeneticandevolutionarystudies AT luisrubio detectionofpersistentvirusesbyhighthroughputsequencingintomatoandpepperfrompanamaphylogeneticandevolutionarystudies
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Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies

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