A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typ...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Ursula Oggenfuss, Thomas Badet, Thomas Wicker, Fanny E Hartmann, Nikhil Kumar Singh, Leen Abraham, Petteri Karisto, Tiziana Vonlanthen, Christopher Mundt, Bruce A McDonald, Daniel Croll
Formato:	article
Lenguaje:	EN
Publicado:	eLife Sciences Publications Ltd 2021
Materias:	Zymoseptoria tritici transposable elements genome evolution population genomics fungi Medicine R Science Q Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/f8a534c8ab65452484980ce5e8202dff
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f8a534c8ab65452484980ce5e8202dff
record_format	dspace
spelling	oai:doaj.org-article:f8a534c8ab65452484980ce5e8202dff2021-11-26T11:14:45ZA population-level invasion by transposable elements triggers genome expansion in a fungal pathogen10.7554/eLife.692492050-084Xe69249https://doaj.org/article/f8a534c8ab65452484980ce5e8202dff2021-09-01T00:00:00Zhttps://elifesciences.org/articles/69249https://doaj.org/toc/2050-084XGenome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen’s center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.Ursula OggenfussThomas BadetThomas WickerFanny E HartmannNikhil Kumar SinghLeen AbrahamPetteri KaristoTiziana VonlanthenChristopher MundtBruce A McDonaldDaniel CrolleLife Sciences Publications LtdarticleZymoseptoria triticitransposable elementsgenome evolutionpopulation genomicsfungiMedicineRScienceQBiology (General)QH301-705.5ENeLife, Vol 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Zymoseptoria tritici transposable elements genome evolution population genomics fungi Medicine R Science Q Biology (General) QH301-705.5
spellingShingle	Zymoseptoria tritici transposable elements genome evolution population genomics fungi Medicine R Science Q Biology (General) QH301-705.5 Ursula Oggenfuss Thomas Badet Thomas Wicker Fanny E Hartmann Nikhil Kumar Singh Leen Abraham Petteri Karisto Tiziana Vonlanthen Christopher Mundt Bruce A McDonald Daniel Croll A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
description	Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen’s center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.
format	article
author	Ursula Oggenfuss Thomas Badet Thomas Wicker Fanny E Hartmann Nikhil Kumar Singh Leen Abraham Petteri Karisto Tiziana Vonlanthen Christopher Mundt Bruce A McDonald Daniel Croll
author_facet	Ursula Oggenfuss Thomas Badet Thomas Wicker Fanny E Hartmann Nikhil Kumar Singh Leen Abraham Petteri Karisto Tiziana Vonlanthen Christopher Mundt Bruce A McDonald Daniel Croll
author_sort	Ursula Oggenfuss
title	A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
title_short	A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
title_full	A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
title_fullStr	A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
title_full_unstemmed	A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
title_sort	population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
publisher	eLife Sciences Publications Ltd
publishDate	2021
url	https://doaj.org/article/f8a534c8ab65452484980ce5e8202dff
work_keys_str_mv	AT ursulaoggenfuss apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT thomasbadet apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT thomaswicker apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT fannyehartmann apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT nikhilkumarsingh apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT leenabraham apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT petterikaristo apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT tizianavonlanthen apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT christophermundt apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT bruceamcdonald apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT danielcroll apopulationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT ursulaoggenfuss populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT thomasbadet populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT thomaswicker populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT fannyehartmann populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT nikhilkumarsingh populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT leenabraham populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT petterikaristo populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT tizianavonlanthen populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT christophermundt populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT bruceamcdonald populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen AT danielcroll populationlevelinvasionbytransposableelementstriggersgenomeexpansioninafungalpathogen
_version_	1718409572426711040

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

Ejemplares similares