Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America

The global banana industry is threatened by one of the most devastating diseases: Fusarium wilt (FWB). FWB is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), which almost annihilated the banana production in the late 1950s. A new strain of Foc, known as tropical race 4 (TR4)...

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Autores principales:	Reyes Herrera, Paula H., Torres Bedoya, Eliana, Lopez Alvarez, Diana, Burbano David, Diana, Carmona, Sandra L., Bebber, Daniel P., Studholme, David J., Betancourt, Monica, Soto Suarez, Mauricio
Formato:	article
Lenguaje:	Inglés
Publicado:	Cold Sprimg Harbor Laboratory - CSH 2025
Materias:	Enfermedades de las plantas - H20 Musa (bananos) Fusarium Marchitez Enfermedades de las plantas Frutales http://aims.fao.org/aos/agrovoc/c_29128 http://aims.fao.org/aos/agrovoc/c_3156 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_5962
Acceso en línea:	https://www.biorxiv.org/content/10.1101/2022.01.17.476647v2 http://hdl.handle.net/20.500.12324/40598 https://doi.org/10.1101/2022.01.17.476647

id	RepoAGROSAVIA40598
record_format	dspace
institution	Corporación Colombiana de Investigación Agropecuaria
collection	Repositorio AGROSAVIA
language	Inglés
topic	Enfermedades de las plantas - H20 Musa (bananos) Fusarium Marchitez Enfermedades de las plantas Frutales http://aims.fao.org/aos/agrovoc/c_29128 http://aims.fao.org/aos/agrovoc/c_3156 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_5962
spellingShingle	Enfermedades de las plantas - H20 Musa (bananos) Fusarium Marchitez Enfermedades de las plantas Frutales http://aims.fao.org/aos/agrovoc/c_29128 http://aims.fao.org/aos/agrovoc/c_3156 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_5962 Reyes Herrera, Paula H. Torres Bedoya, Eliana Lopez Alvarez, Diana Burbano David, Diana Carmona, Sandra L. Bebber, Daniel P. Studholme, David J. Betancourt, Monica Soto Suarez, Mauricio Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America
description	The global banana industry is threatened by one of the most devastating diseases: Fusarium wilt (FWB). FWB is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), which almost annihilated the banana production in the late 1950s. A new strain of Foc, known as tropical race 4 (TR4), attacks a wide range of banana varieties including Cavendish clones which are the source of 99% of banana exports. In 2019, Foc TR4 was reported in Colombia, and more recently (2021) in Peru. In this study, we sequenced three fungal isolates identified as Foc TR4 from La Guajira (Colombia) and compared them against 19 whole-genome sequences of Foc TR4 publicly available, including four genome sequences recently released from Peru. To understand the genetic relatedness of the Colombian Foc TR4 isolates and those from Peru, we conducted a phylogenetic analysis based on a genome-wide set of single nucleotide polymorphisms (SNPs). Additionally, we compared the genomes of the 22 available Foc TR4 isolates looking for the presence-absence of gene polymorphisms and genomic regions. Our results reveal that (i) the Colombian and Peruvian isolates are genetically distant, which could be better explained by independent incursions of the pathogen to the continent, and (ii) there is a high correspondence between the genetic relatedness and geographic origin of Foc TR4. The profile of present/absent genes and the distribution of missing genomic regions showed a high correspondence to the clades recovered in the phylogenetic analysis, supporting the results obtained by SNP-based phylogeny.
format	article
author	Reyes Herrera, Paula H. Torres Bedoya, Eliana Lopez Alvarez, Diana Burbano David, Diana Carmona, Sandra L. Bebber, Daniel P. Studholme, David J. Betancourt, Monica Soto Suarez, Mauricio
author_facet	Reyes Herrera, Paula H. Torres Bedoya, Eliana Lopez Alvarez, Diana Burbano David, Diana Carmona, Sandra L. Bebber, Daniel P. Studholme, David J. Betancourt, Monica Soto Suarez, Mauricio
author_sort	Reyes Herrera, Paula H.
title	Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America
title_short	Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America
title_full	Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America
title_fullStr	Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America
title_full_unstemmed	Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America
title_sort	genome sequence data reveal at least two distinct incursions of the tropical race 4 (tr4) variant of fusarium wilt into south america
publisher	Cold Sprimg Harbor Laboratory - CSH
publishDate	2025
url	https://www.biorxiv.org/content/10.1101/2022.01.17.476647v2 http://hdl.handle.net/20.500.12324/40598 https://doi.org/10.1101/2022.01.17.476647
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spelling	RepoAGROSAVIA405982025-05-16T13:28:41Z Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America Reyes Herrera, Paula H. Torres Bedoya, Eliana Lopez Alvarez, Diana Burbano David, Diana Carmona, Sandra L. Bebber, Daniel P. Studholme, David J. Betancourt, Monica Soto Suarez, Mauricio Enfermedades de las plantas - H20 Musa (bananos) Fusarium Marchitez Enfermedades de las plantas Frutales http://aims.fao.org/aos/agrovoc/c_29128 http://aims.fao.org/aos/agrovoc/c_3156 http://aims.fao.org/aos/agrovoc/c_8391 http://aims.fao.org/aos/agrovoc/c_5962 The global banana industry is threatened by one of the most devastating diseases: Fusarium wilt (FWB). FWB is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), which almost annihilated the banana production in the late 1950s. A new strain of Foc, known as tropical race 4 (TR4), attacks a wide range of banana varieties including Cavendish clones which are the source of 99% of banana exports. In 2019, Foc TR4 was reported in Colombia, and more recently (2021) in Peru. In this study, we sequenced three fungal isolates identified as Foc TR4 from La Guajira (Colombia) and compared them against 19 whole-genome sequences of Foc TR4 publicly available, including four genome sequences recently released from Peru. To understand the genetic relatedness of the Colombian Foc TR4 isolates and those from Peru, we conducted a phylogenetic analysis based on a genome-wide set of single nucleotide polymorphisms (SNPs). Additionally, we compared the genomes of the 22 available Foc TR4 isolates looking for the presence-absence of gene polymorphisms and genomic regions. Our results reveal that (i) the Colombian and Peruvian isolates are genetically distant, which could be better explained by independent incursions of the pathogen to the continent, and (ii) there is a high correspondence between the genetic relatedness and geographic origin of Foc TR4. The profile of present/absent genes and the distribution of missing genomic regions showed a high correspondence to the clades recovered in the phylogenetic analysis, supporting the results obtained by SNP-based phylogeny. 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J., Kay, W., Jeffries, A., O’Neill, P., Farbos, A., Moore, K., et al. 2019. High-quality draft genome sequence of the causal agent of the current Panama disease epidemic. Microbiol. Resour. Announc. 8:e00904–19. ↵Zheng, S.-J., García-Bastidas, F. A., Li, X., Zeng, L., Bai, T., Xu, S., et al. 2018. New Geographical Insights of the Latest Expansion of Fusarium oxysporum f.sp. cubense Tropical Race 4 Into the Greater Mekong Subregion. Front. Plant Sci. 9:1–9 Attribution-NonCommercial-ShareAlike 4.0 International http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf application/pdf Colombia Cold Sprimg Harbor Laboratory - CSH bioRxiv; (2022): bioRxiv (Jan);p. 1 -22.

Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America

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