Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium

Research output: Chapter in Book/Report/Conference proceedingAbstract

Abstract

Genome plasticity enables organisms to adapt to environmental changes and to occupy novel niches. This is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale chromosomal variations, all of which contribute to differences in chromosomal size, organization and gene content. While these mechanisms operate in all organisms, they are particularly relevant for plant pathogens that engage in a co-evolutionary arms race with their hosts. Plant pathogens secrete so-called effectors that contribute to host colonization and counteract host immunity. Effector genes often cluster in highly plastic, transposon-rich genomic regions. However, mechanistic understanding of the evolution of these plastic genomic regions remains scarce. We study these molecular mechanisms in the fungal genus Verticillium that contains economically and ecologically important plant pathogens, among which Verticillium dahliae is the most notorious pathogen that causes vascular wilt disease on >200 plant species. Using long-read sequencing technology, we completely assembled two V. dahliae strains. By comparative genomics, we established that transposable elements play important roles in shaping the genome of V. dahliae. Plastic genomic regions in V. dahliae that contain all known effectors evolve by extensive genomic rearrangements that are mediated by erroneous double-strand breaks, often over transposons. Extensive genomic rearrangements are not only restricted to V. dahliae, but also occur in related Verticillium species. Furthermore, recent segmental duplications are enhanced in the plastic regions. These regions, in contrast to the core genome, are also enriched in active transposons that further contribute to local plasticity. In fungi, transposons are located in tightly condensed chromatin, so called heterochromatin, that is supposed to suppress transposon activity and repress structural variations. In contrast, many fungal pathogens have highly plastic transposon-rich regions. Therefore, research into chromatin opens new avenues to link genome organization, genome plasticity and adaptive genome evolution in fungal pathogens.
Original languageEnglish
Title of host publicationAbstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017
PublisherGenetics Society of America
Pages80-81
Publication statusPublished - 2017
Event29th Fungal Genetics Conference - Asilomar Conference Center, Pacific Grove, CA, United States
Duration: 14 Mar 201719 Mar 2017
http://www.genetics-gsa.org/fungal/2017/Abstract%20Book%202017%208x10.pdf

Conference

Conference29th Fungal Genetics Conference
CountryUnited States
CityPacific Grove, CA
Period14/03/1719/03/17
Internet address

Fingerprint

vascular wilt
Verticillium
transposons
Verticillium dahliae
genome
pathogens
genomics
plastics
plant pathogens
chromatin
organisms
heterochromatin
multigene family
single nucleotide polymorphism
niches
immunity
fungi

Cite this

Seidl, M. F., Faino, L., Cook III, D. E., Kramer, H. M., Shi-Kunne, X., van den Berg-Velthuis, G. C. M., & Thomma, B. P. H. J. (2017). Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium. In Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017 (pp. 80-81). Genetics Society of America.
Seidl, M.F. ; Faino, L. ; Cook III, D.E. ; Kramer, H.M. ; Shi-Kunne, X. ; van den Berg-Velthuis, G.C.M. ; Thomma, B.P.H.J. / Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium. Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. Genetics Society of America, 2017. pp. 80-81
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title = "Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium",
abstract = "Genome plasticity enables organisms to adapt to environmental changes and to occupy novel niches. This is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale chromosomal variations, all of which contribute to differences in chromosomal size, organization and gene content. While these mechanisms operate in all organisms, they are particularly relevant for plant pathogens that engage in a co-evolutionary arms race with their hosts. Plant pathogens secrete so-called effectors that contribute to host colonization and counteract host immunity. Effector genes often cluster in highly plastic, transposon-rich genomic regions. However, mechanistic understanding of the evolution of these plastic genomic regions remains scarce. We study these molecular mechanisms in the fungal genus Verticillium that contains economically and ecologically important plant pathogens, among which Verticillium dahliae is the most notorious pathogen that causes vascular wilt disease on >200 plant species. Using long-read sequencing technology, we completely assembled two V. dahliae strains. By comparative genomics, we established that transposable elements play important roles in shaping the genome of V. dahliae. Plastic genomic regions in V. dahliae that contain all known effectors evolve by extensive genomic rearrangements that are mediated by erroneous double-strand breaks, often over transposons. Extensive genomic rearrangements are not only restricted to V. dahliae, but also occur in related Verticillium species. Furthermore, recent segmental duplications are enhanced in the plastic regions. These regions, in contrast to the core genome, are also enriched in active transposons that further contribute to local plasticity. In fungi, transposons are located in tightly condensed chromatin, so called heterochromatin, that is supposed to suppress transposon activity and repress structural variations. In contrast, many fungal pathogens have highly plastic transposon-rich regions. Therefore, research into chromatin opens new avenues to link genome organization, genome plasticity and adaptive genome evolution in fungal pathogens.",
author = "M.F. Seidl and L. Faino and {Cook III}, D.E. and H.M. Kramer and X. Shi-Kunne and {van den Berg-Velthuis}, G.C.M. and B.P.H.J. Thomma",
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booktitle = "Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017",
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Seidl, MF, Faino, L, Cook III, DE, Kramer, HM, Shi-Kunne, X, van den Berg-Velthuis, GCM & Thomma, BPHJ 2017, Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium. in Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. Genetics Society of America, pp. 80-81, 29th Fungal Genetics Conference, Pacific Grove, CA, United States, 14/03/17.

Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium. / Seidl, M.F.; Faino, L.; Cook III, D.E.; Kramer, H.M.; Shi-Kunne, X.; van den Berg-Velthuis, G.C.M.; Thomma, B.P.H.J.

Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. Genetics Society of America, 2017. p. 80-81.

Research output: Chapter in Book/Report/Conference proceedingAbstract

TY - CHAP

T1 - Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium

AU - Seidl, M.F.

AU - Faino, L.

AU - Cook III, D.E.

AU - Kramer, H.M.

AU - Shi-Kunne, X.

AU - van den Berg-Velthuis, G.C.M.

AU - Thomma, B.P.H.J.

PY - 2017

Y1 - 2017

N2 - Genome plasticity enables organisms to adapt to environmental changes and to occupy novel niches. This is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale chromosomal variations, all of which contribute to differences in chromosomal size, organization and gene content. While these mechanisms operate in all organisms, they are particularly relevant for plant pathogens that engage in a co-evolutionary arms race with their hosts. Plant pathogens secrete so-called effectors that contribute to host colonization and counteract host immunity. Effector genes often cluster in highly plastic, transposon-rich genomic regions. However, mechanistic understanding of the evolution of these plastic genomic regions remains scarce. We study these molecular mechanisms in the fungal genus Verticillium that contains economically and ecologically important plant pathogens, among which Verticillium dahliae is the most notorious pathogen that causes vascular wilt disease on >200 plant species. Using long-read sequencing technology, we completely assembled two V. dahliae strains. By comparative genomics, we established that transposable elements play important roles in shaping the genome of V. dahliae. Plastic genomic regions in V. dahliae that contain all known effectors evolve by extensive genomic rearrangements that are mediated by erroneous double-strand breaks, often over transposons. Extensive genomic rearrangements are not only restricted to V. dahliae, but also occur in related Verticillium species. Furthermore, recent segmental duplications are enhanced in the plastic regions. These regions, in contrast to the core genome, are also enriched in active transposons that further contribute to local plasticity. In fungi, transposons are located in tightly condensed chromatin, so called heterochromatin, that is supposed to suppress transposon activity and repress structural variations. In contrast, many fungal pathogens have highly plastic transposon-rich regions. Therefore, research into chromatin opens new avenues to link genome organization, genome plasticity and adaptive genome evolution in fungal pathogens.

AB - Genome plasticity enables organisms to adapt to environmental changes and to occupy novel niches. This is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale chromosomal variations, all of which contribute to differences in chromosomal size, organization and gene content. While these mechanisms operate in all organisms, they are particularly relevant for plant pathogens that engage in a co-evolutionary arms race with their hosts. Plant pathogens secrete so-called effectors that contribute to host colonization and counteract host immunity. Effector genes often cluster in highly plastic, transposon-rich genomic regions. However, mechanistic understanding of the evolution of these plastic genomic regions remains scarce. We study these molecular mechanisms in the fungal genus Verticillium that contains economically and ecologically important plant pathogens, among which Verticillium dahliae is the most notorious pathogen that causes vascular wilt disease on >200 plant species. Using long-read sequencing technology, we completely assembled two V. dahliae strains. By comparative genomics, we established that transposable elements play important roles in shaping the genome of V. dahliae. Plastic genomic regions in V. dahliae that contain all known effectors evolve by extensive genomic rearrangements that are mediated by erroneous double-strand breaks, often over transposons. Extensive genomic rearrangements are not only restricted to V. dahliae, but also occur in related Verticillium species. Furthermore, recent segmental duplications are enhanced in the plastic regions. These regions, in contrast to the core genome, are also enriched in active transposons that further contribute to local plasticity. In fungi, transposons are located in tightly condensed chromatin, so called heterochromatin, that is supposed to suppress transposon activity and repress structural variations. In contrast, many fungal pathogens have highly plastic transposon-rich regions. Therefore, research into chromatin opens new avenues to link genome organization, genome plasticity and adaptive genome evolution in fungal pathogens.

M3 - Abstract

SP - 80

EP - 81

BT - Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017

PB - Genetics Society of America

ER -

Seidl MF, Faino L, Cook III DE, Kramer HM, Shi-Kunne X, van den Berg-Velthuis GCM et al. Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium. In Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. Genetics Society of America. 2017. p. 80-81