Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila

Gabriel E. Rech, Santiago Radío, Sara Guirao-Rico, Laura Aguilera, Vivien Horvath, Llewellyn Green, Hannah Lindstadt, Véronique Jamilloux, Hadi Quesneville and Josefa González ()
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Gabriel E. Rech: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
Santiago Radío: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
Sara Guirao-Rico: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
Laura Aguilera: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
Vivien Horvath: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
Llewellyn Green: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
Hannah Lindstadt: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)
Véronique Jamilloux: Université Paris-Saclay, INRAE, URGI
Hadi Quesneville: Université Paris-Saclay, INRAE, URGI
Josefa González: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra)

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.

Date: 2022
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DOI: 10.1038/s41467-022-29518-8

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