De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology.

Jacob E. Crawford (1) , Wamdaogo M. Guelbeogo (2) , Antoine Sanou (2) , Alphonse Traore (2) , Kenneth D Vernick (3, 4) , N'Fale Sagnon (2) , Brian P. Lazzaro (1)

1 Cornell University [New York]
2 CNRFP - Centre National de Recherche et de Formation sur le Paludisme [Ouagadougou, Burkina Faso]
3 Génétique et Génomique des Insectes vecteurs
4 UMN - University of Minnesota [Twin Cities]

BACKGROUND: Anopheles funestus is one of the primary vectors of human malaria, which causes a million deaths each year in sub-Saharan Africa. Few scientific resources are available to facilitate studies of this mosquito species and relatively little is known about its basic biology and evolution, making development and implementation of novel disease control efforts more difficult. The An. funestus genome has not been sequenced, so in order to facilitate genome-scale experimental biology, we have sequenced the adult female transcriptome of An. funestus from a newly founded colony in Burkina Faso, West Africa, using the Illumina GAIIx next generation sequencing platform. METHODOLOGY/PRINCIPAL FINDINGS: We assembled short Illumina reads de novo using a novel approach involving iterative de novo assemblies and "target-based" contig clustering. We then selected a conservative set of 15,527 contigs through comparisons to four Dipteran transcriptomes as well as multiple functional and conserved protein domain databases. Comparison to the Anopheles gambiae immune system identified 339 contigs as putative immune genes, thus identifying a large portion of the immune system that can form the basis for subsequent studies of this important malaria vector. We identified 5,434 1:1 orthologues between An. funestus and An. gambiae and found that among these 1:1 orthologues, the protein sequence of those with putative immune function were significantly more diverged than the transcriptome as a whole. Short read alignments to the contig set revealed almost 367,000 genetic polymorphisms segregating in the An. funestus colony and demonstrated the utility of the assembled transcriptome for use in

Mots clés: *Sequence Analysis; RNA; Animals; Anopheles/*metabolism; Cluster Analysis; Computational Biology; Contig Mapping; Expressed Sequence Tags; Female; Gene Expression Profiling; Insect Vectors; Malaria/*parasitology; Polymorphism; Genetic; Single Nucleotide; RNA/*metabolism

Domaines: Parasitologie; Santé publique et épidémiologie; Zoologie des invertébrés

Jacob E. Crawford, Wamdaogo M. Guelbeogo, Antoine Sanou, Alphonse Traore, Kenneth D Vernick, et al.. De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology.. PLoS ONE, 2010, 5 (12), pp.e14202. ⟨10.1371/journal.pone.0014202⟩. ⟨pasteur-02008335⟩