Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes
Rius Camps, Nuria (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Guillén, Yolanda (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Delprat Obeaga, Alejandra (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Kapusta, Aurélie (University of Utah School of Medicine. Department of Human Genetics)
Feschotte, Cédric (University of Utah School of Medicine. Department of Human Genetics)
Ruiz, Alfredo, (Ruiz Panadero) (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)

Data:	2016
Resum:	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. The online version of this article (doi:10. 1186/s12864-016-2648-8) contains supplementary material, which is available to authorized users.
Ajuts:	Ministerio de Ciencia e Innovación BFU2011-30476 Ministerio de Ciencia e Innovación BFU2008-04988
Nota:	Altres ajuts: This work was supported by grant R01GM077582 to C.F from the National Institutes of Health, and by PIF-UAB fellowship to N.R.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Drosophila ; Buzzatii ; Transposable elements ; Genome
Publicat a:	BMC genomics, Vol. 17 (2016) , art. 344, ISSN 1471-2164

DOI: 10.1186/s12864-016-2648-8
PMID: 27164953

14 p, 1.6 MB

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