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Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families

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Abstract

The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron). We propose the existence of novel families: Hypo, belonging to the LTR Gypsy superfamily; Hamp, belonging to non-LTRs; and rosa, belonging to Class II or DNA transposons. Although the rosa clade has been previously described, it was considered to be a basal subfamily of the mariner family. Based on our phylogenetic analysis, including Tc1, mariner, pogo, rosa and Lsra elements from other insects, we propose that rosa and Lsra elements are subfamilies of an independent family of Class II elements termed rosa. The annotations obtained indicate that a low percentage of the assembled CBB genome (approximately 8.2%) consists of TEs. Although these TEs display high diversity, most sequences are degenerate, with few full-length copies of LTR and DNA transposons and several complete and putatively active copies of non-LTR elements. MITEs constitute approximately 50% of the total TEs content, with a high proportion associated with DNA transposons in the Tc1-mariner superfamily.

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Abbreviations

APE:

Apurinic/apyrimidinic endonuclease

BLAST:

Basic local alignment search tool

CBB:

Coffee berry borer

GtRNAdb:

Genomic tRNA Database

GyDB:

Gypsy database

HSP:

High-scoring segment pairs

LINE:

Long interspersed element

LTR:

Long terminal repeat

MITEs:

Miniature inverted–repeat transposable elements

ORFs:

Open reading frames

pHMMs:

Profile hidden Markov models

RNaseH:

Ribonuclease H

RT:

Reverse transcriptase

TEs:

Transposable elements

TIR:

Terminal inverted repeat

TSD:

Target site duplication

WGS:

Whole-genome sequence

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Acknowledgements

We gratefully acknowledge funding from the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, Grant No. 2013/15070-4) and from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Grant No. 306493/2013-6) to CMAC, FAPESP fellowship Grant No. 12/24813-8 to EHH, fellowship from Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro (CAPES/FAPERJ) to RDFM and Ministerio de Agricultura y Desarrollo Rural de Colombia to PBM, JN and LNE.

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Authors and Affiliations

  1. UNESP-Univ. Estadual Paulista, São José do Rio Preto, SP, Brazil

    Eric M. Hernandez-Hernandez & Claudia M. A. Carareto

  2. Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil

    Rita Daniela Fernández-Medina

  3. National Coffee Research Center-CENICAFÉ, Manizales, Colombia

    Lucio Navarro-Escalante & Pablo Benavides-Machado

  4. Purdue University, West Lafayette, IN, USA

    Lucio Navarro-Escalante

  5. CIAT-International Center for Tropical Agriculture, Cali, Colombia

    Jonathan Nuñez

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  1. Eric M. Hernandez-Hernandez
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Correspondence to Claudia M. A. Carareto.

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Author EMHH, author RDFM, author LNE, author JN, author PBM and author CMAC declare that they have no conflict of interest.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. This article does not contain any studies with human participants or animals performed by any of the authors.

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Communicated by S. Hohmann.

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Hernandez-Hernandez, E.M., Fernández-Medina, R.D., Navarro-Escalante, L. et al. Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families. Mol Genet Genomics 292, 565–583 (2017). https://doi.org/10.1007/s00438-017-1291-7

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