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

• Published in: Nature communications 2022-04, Vol.13 (1), p.1948-16, Article 1948
• Main Authors: Rech, Gabriel E., Radío, Santiago, Guirao-Rico, Sara, Aguilera, Laura, Horvath, Vivien, Green, Llewellyn, Lindstadt, Hannah, Jamilloux, Véronique, Quesneville, Hadi, González, Josefa
• Format: Article
• Language: English
• Subjects: 38/91; 45/22; 45/23; 631/181/2474; 631/208/182; 631/208/199; 64/24; Animals; Biochemistry, Molecular Biology; Biodiversity; Biological evolution; DNA Transposable Elements - genetics; Drosophila; Drosophila - genetics; Drosophila melanogaster - genetics; Evolution; Evolution & development; Evolution, Molecular; Fruit flies; Gene Expression; Genetic diversity; Genomes; Genomics; Humanities and Social Sciences; Insects; Life Sciences; multidisciplinary; Natural populations; Population genetics; Population studies; Populations; Populations and Evolution; Science; Science (multidisciplinary); Sequence Analysis, DNA; Species; Structure-function relationships; Transposons; Wildlife conservation
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-29518-8

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. Even in well-studied species, there is still substantial natural genetic variation that has not been characterized. Here, the authors use long read sequencing to discover transposable elements in the Drosophila genome not detected by short read sequencing, and link them to gene expression.