Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

Research output: Contribution to journalArticleAcademicpeer-review

13 Citations (Scopus)

Abstract

Background: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Results: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. Conclusions: The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.
LanguageEnglish
Article number735
JournalBMC Genomics
Volume18
Issue number1
DOIs
Publication statusPublished - 2017

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Mitochondrial Genome
Fusarium
Genetic Recombination
Population Genetics
Introns
Genome

Keywords

  • Comparative genomics
  • Mitochondrial genome
  • Mitochondrial recombination
  • Phylogenomics

Cite this

@article{362cb51ea0274d0bad3d412d4858841e,
title = "Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex",
abstract = "Background: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Results: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. Conclusions: The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.",
keywords = "Comparative genomics, Mitochondrial genome, Mitochondrial recombination, Phylogenomics",
author = "Bal{\'a}zs Brankovics and {van Dam}, Peter and Martijn Rep and {de Hoog}, G.S. and {van der Lee}, {Theo A.J.} and Cees Waalwijk and {van Diepeningen}, {Anne D.}",
year = "2017",
doi = "10.1186/s12864-017-4116-5",
language = "English",
volume = "18",
journal = "BMC Genomics",
issn = "1471-2164",
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Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex. / Brankovics, Balázs; van Dam, Peter; Rep, Martijn; de Hoog, G.S.; van der Lee, Theo A.J.; Waalwijk, Cees; van Diepeningen, Anne D.

In: BMC Genomics, Vol. 18, No. 1, 735, 2017.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

AU - Brankovics, Balázs

AU - van Dam, Peter

AU - Rep, Martijn

AU - de Hoog, G.S.

AU - van der Lee, Theo A.J.

AU - Waalwijk, Cees

AU - van Diepeningen, Anne D.

PY - 2017

Y1 - 2017

N2 - Background: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Results: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. Conclusions: The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

AB - Background: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Results: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. Conclusions: The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

KW - Comparative genomics

KW - Mitochondrial genome

KW - Mitochondrial recombination

KW - Phylogenomics

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