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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, and  D. mojavensis .    Results  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.    Conclusions  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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2648-8) contains supplementary material, which is available to authorized users.

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes