title: Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.
abstract: Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis.
  
  
  
  We have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of the D. buzzatii st-1 genome is made up of TEs, between 7 and 7,5 % of D. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes.
  
  
  
  TEs in D. buzzatii are less abundant than in D. mojavensis, as expected according to the genome size and TE content positive correlation. However, TEs alone do not explain the genome size difference. TEs accumulate in the dot chromosomes and proximal regions of D. buzzatii and D. mojavensis chromosomes. We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families in D. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy.
authors.affiliation: Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain. nuria.rius.camps@gmail.com.
authors.forename: Nuria
authors.initials: N
authors.lastname: Rius
authors.affiliation: Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Guillén
authors.affiliation: Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Delprat
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Kapusta
authors.affiliation: Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: Cédric
authors.initials: C
authors.lastname: Feschotte
authors.affiliation: Department de Genética i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Ruiz
mesh_terms: D000818:Animals; D059006:Chromosomes, Insect; D004251:DNA Transposable Elements; D004330:Drosophila / Q000235:genetics*; D049750:Genome, Insect; D023281:Genomics / Q000379:methods; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements
keywords: Buzzatii; Drosophila; Genome; Transposable elements