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Transposable elements in the Anopheles funestus transcriptome

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Abstract

Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized. Interestingly, we have identified a full-length putative active element (including the presence of full length TIRs in the genomic sequence) belonging to the hAT superfamily, which presents active members in other insect genomes. This work contributes to a comprehensive understanding of the landscape of transposable elements in A. funestus transcriptome. Our results reveal that TEs are abundant and diverse in the mosquito and that most of the TE families found in the genome are represented in the mosquito transcriptome, a fact that could indicate activity of these elements.The vast diversity of TEs expressed in A. funestus suggests that there is ongoing amplification of several families in this organism.

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Abbreviations

CDS:

Coding sequence

Db:

Database

LTR:

Long terminal repeat

MITE:

Miniature inverted repeat transposable elements

NLTR:

Non-long terminal repeat

ORF:

Open reading frame

PSI-Blast:

Position-specific iterated BLAST

RB:

Repbase

RPS-Blast:

Reverse position-specific BLAST

TE:

Transposable elements

TIR:

Terminal inverted repeat

TSD:

Terminal site duplications

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Acknowledgements

R.D.F.M. has a postdoctoral position supported by Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro (FAPERJ) and Comissão de Aperfeiçoamento de Pessoal do Nível Superior (CAPES). J.M.C.R was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases. Because JMCR is a government employees and this is a government work, the work is in the public domain in the United States. Notwithstanding any other agreements, the NIH reserves the right to provide the work to PubMedCentral for display and use by the public, and PubMedCentral may tag or modify the work consistent with its customary practices. You can establish rights outside of the U.S. subject to a government use license. C.M.A.C. was supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Grant 306493/2013-6 and CJS was partially funded by CNPq and FAPERJ.

Author contributions

Conceived the study: RDFM, CMAC, JMR and CJS. Analyzed the data and wrote the paper: RDFM. All authors read and approved the final manuscript.

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Authors and Affiliations

  1. Fundação Oswaldo Cruz, Escola Nacional de Saúde Pública, Av. Brasil, 4365, Rio de Janeiro, Brazil

    Rita D. Fernández-Medina & Cláudio J. Struchiner

  2. Departamento de Biologia, UNESP-Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265, São José do Rio Preto, SP, Brazil

    Claudia M. A. Carareto

  3. Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD, 20852, USA

    José M. C. Ribeiro

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  1. Rita D. Fernández-Medina
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  2. Claudia M. A. Carareto
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  3. Cláudio J. Struchiner
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  4. José M. C. Ribeiro
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Correspondence to Rita D. Fernández-Medina.

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Fernández-Medina, R.D., Carareto, C.M.A., Struchiner, C.J. et al. Transposable elements in the Anopheles funestus transcriptome. Genetica 145, 275–293 (2017). https://doi.org/10.1007/s10709-017-9964-z

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