Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations.
Classification
Fungi
Genome defense
Retrotransposons
Transposable elements
Journal
Mobile DNA
ISSN: 1759-8753
Titre abrégé: Mob DNA
Pays: England
ID NLM: 101519891
Informations de publication
Date de publication:
13 Jan 2024
13 Jan 2024
Historique:
received:
31
10
2023
accepted:
22
12
2023
medline:
14
1
2024
pubmed:
14
1
2024
entrez:
13
1
2024
Statut:
epublish
Résumé
The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5' half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged species-complex, which makes the system ideal to classify the crapaud family based on the observed LTR variation and to study the evolutionary dynamics, such as the diversification and bursts of the elements over recent evolutionary time. We developed a sequence similarity network approach to classify the crapaud repeats of seven genomes representing the P. anserina species complex into 14 subfamilies. This method does not utilize a consensus sequence, but instead it connects any copies that share enough sequence similarity over a set sequence coverage. Based on phylogenetic analyses, we found that the crapaud repeats likely diversified in the ancestor of the complex and have had activity at different time points for different subfamilies. Furthermore, while we hypothesized that the evolution into multiple subfamilies could have been a direct effect of escaping the genome defense system of repeat induced point mutations, we found this not to be the case. Our study contributes to the development of methods to classify transposable elements in fungi, and also highlights the intricate patterns of retrotransposon evolution over short timescales and under high mutational load caused by nucleotide-altering genome defense.
Sections du résumé
BACKGROUND
BACKGROUND
The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5' half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged species-complex, which makes the system ideal to classify the crapaud family based on the observed LTR variation and to study the evolutionary dynamics, such as the diversification and bursts of the elements over recent evolutionary time.
RESULTS
RESULTS
We developed a sequence similarity network approach to classify the crapaud repeats of seven genomes representing the P. anserina species complex into 14 subfamilies. This method does not utilize a consensus sequence, but instead it connects any copies that share enough sequence similarity over a set sequence coverage. Based on phylogenetic analyses, we found that the crapaud repeats likely diversified in the ancestor of the complex and have had activity at different time points for different subfamilies. Furthermore, while we hypothesized that the evolution into multiple subfamilies could have been a direct effect of escaping the genome defense system of repeat induced point mutations, we found this not to be the case.
CONCLUSIONS
CONCLUSIONS
Our study contributes to the development of methods to classify transposable elements in fungi, and also highlights the intricate patterns of retrotransposon evolution over short timescales and under high mutational load caused by nucleotide-altering genome defense.
Identifiants
pubmed: 38218923
doi: 10.1186/s13100-023-00311-8
pii: 10.1186/s13100-023-00311-8
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1Subventions
Organisme : Vetenskapsrådet
ID : 2021-04290
Organisme : Vetenskapsrådet
ID : 2019-05188
Organisme : Svenska Forskningsrådet Formas
ID : 2019-01227
Informations de copyright
© 2024. The Author(s).
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