Reconstructing the evolutionary history of gypsy retrotransposons in the Périgord black truffle (Tuber melanosporum Vittad.)
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Truffles are ascomycete fungi belonging to genus Tuber, and they form ectomycorrhizal associations with trees and shrubs. Transposable elements constitute more than 50 % of the black Périgord truffle (Tuber melanosporum) genome, which are mainly class 1 gypsy retrotransposons, but their impact on its genome is unknown. The aims of this study are to investigate the diversity of gypsy retrotransposons in this species and their evolutionary history by analysing the reference genome and six resequenced genomes of different geographic accessions. Using the reverse transcriptase sequences, six different gypsy retrotransposon clades were identified. Tmt1 and Tmt6 are the most abundant transposable elements, representing 14 and 13 % of the T. melanosporum genome, respectively. Tmt6 showed a major burst of proliferation between 1 and 4 million years ago, but evidence of more recent transposition was observed. Except for Tmt2, the other clades tend to aggregate, and their mode of transposition excluded the master copy model. This suggests that each new copy has the same probability of transposing as other copies. This study provides a better view of the diversity and dynamic nature of gypsy retrotransposons in T. melanosporum. Even if the major gypsy retrotransposon bursts are old, some elements seem to have transposed recently, suggesting that they may continue to model the truffle genomes.
KeywordsTruffle Transposable elements Chromovirus Gypsy retrotransposons Transposition dynamic
The UMR1136 is supported by a grant overseen by the French National Research Agency (ANR) as part of the ‘Investissements d’Avenir’ program (ANR-11-LABX-0002-01, Lab of Excellence ARBRE). This study benefited from ANR SYSTERRA SYSTRUF (ANR-09-STRA-10). The PhD fellowship of Thibaut Payen is co-funded by the Lorraine Region and the European Commission through the EcoFINDERS project (FP7-264465). We would like to thank Dr. Arnaud Le Rouzic for his critical reading of a previous version of the manuscript.
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