Abstract
BackgroundMany 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.ResultsWe 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.ConclusionsTEs 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 materialThe online version of this article (doi:10.1186/s12864-016-2648-8) contains supplementary material, which is available to authorized users.
Highlights
Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods
Helitrons are the most abundant order in the three genomes, they are more abundant in the D. buzzatii st-1 genome (40.61 % of the Transposable elements (TEs) content) than in the other two genomes (30.65 % in D. buzzatii j-19 and 33.90 % in D. mojavensis)
TIRtransposons are more frequent in D. buzzatii genomes (14.81 % in st-1 and 14.46 % in j-19) than in D. mojavensis (9.24 %), like the unclassified repeats that are more abundant in D. buzzatii (7.15 % in st-1 and 9.11 % in j-19) than in D. mojavensis (2.42 %)
Summary
Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. There are two classes of TEs, those that mobilize via an RNA intermediate belong to class I and those which transpose directly, leaving the donor site, or via a DNA intermediate, to class II [2, 3] Further divisions in this classification comprise orders that distinguish TEs with different insertion mechanisms, and superfamilies that are composed of TEs with similar domain structures and protein sequences. After D. melanogaster [4] and D. pseudoobscura [5] were sequenced, joint efforts provided the research community with the genomes of ten new Drosophila species which allowed multiple species comparisons [6]. These 12 genomes were sequenced with Sanger technology. Six de novo genomes were published individually [7,8,9,10,11,12], and eight more together [13]; these 14 genomes were sequenced mainly with Next-Generation Sequencing (NGS) technology
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
