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Genetica

, Volume 143, Issue 2, pp 225–239 | Cite as

De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease

  • A. Marchant
  • F. Mougel
  • C. Almeida
  • E. Jacquin-Joly
  • J. Costa
  • M. Harry
Article

Abstract

High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, <1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

Keywords

HTS De novo assembly Non-model organisms Chimeric contigs Chagas disease vector Triatoma 

Notes

Acknowledgments

We would like to thank Rachel Legendre and Claire Toffano of Institut de Génétique et Microbiologie CNRS - UMR 8621 who gave us the script for 454 contig correction. We thank Marie-Christine François (iEES, INRA Versailles, France) for help with the T. brasiliensis RNA extractions. The authors are also very grateful to the engineers of the bioinformatics platforms Genouest at the University of Rennes 1 and eBio of the University Paris Sud for technical support. This work has benefited from the facilities and expertise of the HTS platform of IMAGIF (Centre de Recherche de Gif - www.imagif.cnrs.fr. This study was funded by the French Agence Nationale de la Recherche (ADAPTANTHROP project, ANR-097-PEXT-009) and supported by the labex Biodiversité, Agroécosystèmes, Société, Climat (BASC; University Paris Saclay, France). Marchant A. was funded by the Idex Paris Saclay, France.

Conflict of interest

The authors announce that they have not a financial relationship with the organization that sponsored the research. The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  1. 1.Laboratoire Evolution, Génomes et Spéciation LEGS, UPR 9034CNRSGif-sur-YvetteFrance
  2. 2.Université Paris SudOrsayFrance
  3. 3.Departamento de Ciências Biológicas, Faculdade de Ciências FarmacêuticasUNESPAraraquaraBrazil
  4. 4.INRA, UMR 1392Institut d’Ecologie et des Sciences de l’Environnement de ParisVersaillesFrance
  5. 5.Laboratório de Biodiversidade EntomológicaInstituto Oswaldo Cruz, FiocruzRio de JaneiroBrazil

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