Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes. (December 2016)

• Record Type: Journal Article
• Authors: Rius, Nuria; Guillén, Yolanda; Delprat, Alejandra; Kapusta, Aurélie; Feschotte, Cédric; Ruiz, Alfredo
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 14
• Publication Date: 2016-12
• Subjects: Drosophila -- Buzzatii -- Transposable elements -- Genome; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2648-8
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background 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, andD. mojavensis . Results We have sequenced a newD. buzzatii genome (j-19) that complements theD. buzzatii reference genome (st-1) already published, and compared their TE contents with that ofD. mojavensis . We found an underestimation of TE sequences inDrosophila 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 theD. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of theD. buzzatii st-1 genome is made up of TEs, between 7 and 7, 5 % ofD. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes. Conclusions TEs inD. buzzatii are less abundant than inD. 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 ofD. buzzatii andD. mojavensis chromosomes. We also report a significantly higher TE density inD. buzzatii andD. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families inD. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy.