Abstract
Background Anopheles funestus is one of the major malaria vectors in Africa and yet there are few genomic tools available for this species compared to An. gambiae. To start to close this knowledge gap, we sequenced the An. funestus transcriptome using cDNA libraries developed from a pyrethroid resistant laboratory strain and a pyrethroid susceptible field strain from Mali.ResultsUsing a pool of life stages (pupae, larvae, adults: females and males) for each strain, 454 sequencing generated 375,619 reads (average length of 182 bp). De novo assembly generated 18,103 contigs with average length of 253 bp. The average depth of coverage of these contigs was 8.3. In total 20.8% of all reads were novel when compared to reference databases. The sequencing of the field strain generated 204,758 reads compared to 170,861 from the insecticide resistant laboratory strain. The contigs most differentially represented in the resistant strain belong to the P450 gene family and cuticular genes which correlates with previous studies implicating both of these gene families in pyrethroid resistance. qPCR carried out on six contigs indicates that these ESTs could be suitable for gene expression studies such as microarray. 31,000 sites were estimated to contain Single Nucleotide Polymorphisms (SNPs) and analysis of SNPs from 20 contigs suggested that most of these SNPs are likely to be true SNPs. Gene conservation analysis confirmed the close phylogenetic relationship between An. funestus and An. gambiae.ConclusionThis study represents a significant advance for the genetics and genomics of An. funestus since it provides an extensive set of both Expressed Sequence Tags (ESTs) and SNPs which can be readily adopted for the design of new genomic tools such as microarray or SNP platforms.
Highlights
The mosquito Anopheles funestus is a major vector of malaria throughout much of sub-Saharan Africa
For example only 75 microsatellite loci have been identified in An. funestus compared with 300 in An. gambiae ; 600 Single Nucleotide Polymorphisms (SNPs) have been reported for An. funestus [2] compared to 400,000 in An. gambiae and only 2,846 ESTs (Expressed Sequence Tags) have been reported in An. funestus [3] compared to 153,165 in An. gambiae
The sequencing reads have been deposited to National Center for Biotechnology Information (NCBI)’s SRA database with the assembly output (Accession number: SRA009034) and contig sequences have been submitted to the Transcriptome Shotgun Assembly sequence database (TSA) of NCBI
Summary
The mosquito Anopheles funestus is a major vector of malaria throughout much of sub-Saharan Africa. The availability of the high-resolution genetic information in An. gambiae has enabled microarray studies to be carried out in An. gambiae [5,6] in order to elucidate various aspects of the its biology. No such microarrays have been designed for An. funestus. Anopheles funestus is one of the major malaria vectors in Africa and yet there are few genomic tools available for this species compared to An. gambiae. To start to close this knowledge gap, we sequenced the An. funestus transcriptome using cDNA libraries developed from a pyrethroid resistant laboratory strain and a pyrethroid susceptible field strain from Mali
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