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Chromosome Research

, Volume 27, Issue 3, pp 203–219 | Cite as

The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies

  • Pedro M. Fonseca
  • Rafael D. Moura
  • Gabriel L. Wallau
  • Elgion L. S. LoretoEmail author
Original Article

Abstract

The Drosophila genus is one of the main model organisms in evolutionary studies, including those investigating the role of transposable elements (TE) in genomic evolution both at the nucleotide and chromosome levels. D. incompta is a species with restricted ecology, using Cestrum (Solanaceae) flowers as unique sources for oviposition, feeding and development. In the present study, we deeply characterise the D. incompta mobilome and generate a curated dataset. A total of 277 elements were identified, corresponding to approximately 14% of the genome, and 164 of these elements are new, of which 32.62% are putatively autonomous and 8.9% are transcriptionally active in adult flies. The restricted ecology does not seem to influence the dynamics of TE in this fly, since the proportion and diversity of TEs in its genome are similar to that of other Drosophila species. This result is reinforced by the absence of a clear pattern when comparing the TE landscape between generalist and specialist flies. Using 32 available Drosophila genomes—24 ecologically generalist species and 8 specialist species—no difference was found between their TE landscape patterns. However, differences were found between species of the Sophophora and Drosophila subgenus, indicating there are lineage-specific factors shaping TE landscapes.

Keywords

Transposable Elements Niche Amplitude Horizontal Transfer transposons Genome 

Abbreviations

TE

Transposable elements

bp

Base pairs

PA

Putative autonomous

PNA

Putative non-autonomous

DG

Degenerated

TIRs

Terminal inverted repeats

LTRs

Long terminal repeats

TSD

Target site duplication

ORF

Open reading frame

K2P

Kimura two parameters

Notes

Acknowledgements

We are grateful to Dr. Lizandra Robe and two anonymous reviewers for suggestions.

Author contribution statement

PMF and EL conceived and designed research. PMF, RMD and GLW conducted experiments and analysed data. PMF, GLW and EL wrote the manuscript. All authors read and approved the manuscript.

Funding information

This study was supported by research grants and fellowships from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Pronex-Fapergs (16/2551—0000 499-4).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10577_2019_9609_MOESM1_ESM.doc (54 kb)
Supplementary Material 1: A comparison of TE landscapes between specialist and generalist Drosophila. A table (Supplementary Table A) showing all the species used in the phylogenetic and landscape analyses with niche discrimination and group identification. (DOC 54 kb)
10577_2019_9609_MOESM2_ESM.xlsx (467 kb)
Supplementary Table S1: Spreadsheet showing all the D. incompta annotated TEs. Each sheet corresponds to one superfamily. (XLSX 466 kb)
10577_2019_9609_MOESM3_ESM.xlsx (71 kb)
Supplementary Table S2: Spreadsheet showing all the genes used in the phylogenetic and HTT (VHICA) analyses along with their accession codes and sequences. (XLSX 71 kb)
10577_2019_9609_MOESM4_ESM.xlsx (6 kb)
Supplementary Table S3: Statistical data of both genome and transcriptome draft assemblies. (XLSX 5 kb)
10577_2019_9609_MOESM5_ESM.xlsx (12 kb)
Supplementary Table S4: Spreadsheet containing the results of the homology search (BLASTn) of the all annotated D. incompta TEs against the D. incompta transcriptome draft. In this analysis the following threshold values were used: a) percentage of identity of query (annotated TEs) and subject (transcriptome draft scaffolds) = 84%; b) minimum alignment length = 100 bp; c) maximum number of base mismatches per alignment = 10; and d) maximum number of gaps per alignment = 5. (XLSX 12 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Programa de Pós-Graduação em Genética e Biologia MolecularUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
  2. 2.Departamento de Bioquímica e Biologia MolecularUniversidade Federal de Santa Maria (UFSM)Santa MariaBrazil
  3. 3.Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)RecifeBrazil

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