The genome of Anopheles darlingi, the main neotropical malaria vector

Abstract

Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vector-human and vector-parasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles-darlingi.

Figure 1.

Phylogenetic relationships of five dipteran species (adapted from [11]). The evolution relationship and divergence time of A. darlingi in comparison with species of the Anopheles, Aedes, Culex and Drosophila genera.

Figure 2.

Comparison of gene organization between A. darlingi, A. gambiae and D. melanogaster. (A) Gene distribution along A. gambiae chromosomes and the location of their respective orthologs on the 12 largest A. darlingi scaffolds. Black-edged vertical and horizontal bars represent A. gambiae and A. darlingi chromosomes and scaffolds. Colored lines within each bar indicate the location and strand of genes: the leftmost or uppermost column indicates the plus strand; the rightmost or bottommost column indicates the minus strand. The color of those genes denotes either the chromosome where A. gambiae genes are encoded or, in the case of lines representing A. darlingi genes, the A. gambiae chromosome where their respective orthologs are encoded. Gray colored lines represent either A. darlingi genes without orthologs in A. gambiae or genes with two or more homologs in distinct A. gambiae chromosomes. (B) Gene distribution along D. melanogaster chromosomes and the 12 largest A. darlingi scaffolds. The results are presented in a schema equivalent to the one on panel A. (C) Distribution of A. darlingi orthologous genes along A. gambiae chromosome 2R. The five scaffolds with the longest alignment against chromosome 2R are depicted here. Each row contains black-edged horizontal bars representing either chromosomes (A. gambiae) or genomic scaffolds (A. darlingi). The green lines indicate the position and strand of the genes. The gray projections connect orthologous genes across organisms. Some of A. darlingi scaffolds had their orientation modified to facilitate the visualization of syntenic blocks.

Figure 3.

Synteny clusters statistics. (A) Distribution of the number of genes per synteny cluster when considering A. darlingi (Ad) versus either A. gambiae (Ag), A. aegypti (Aa), C. quinquefasciatus (Cq) or D. melanogaster (Dm). Data points represent synteny clusters with more than three protein-coding genes on each pairwise comparison. The points were scattered in each column for the purpose of facilitating visualization. Red horizontal lines indicate the media values of the distribution. (B) The total number of syntenic genes between each pair of species. (C) Number of synteny clusters identified on each comparison. The whole extent of the bars indicates the total number of clusters that were identified in each analysis, which was further divided into clusters located internally on scaffolds or chromosomes versus those near chromosomes or scaffold ends. Species names were abbreviated, as in panel A.

Figure 4.

Distribution and functional categories of protein-coding genes predicted in Anopheles species. The best matches distribution of all (10 481) of the A. darlingi predicted protein coding genes in the KEGG database, by organisms; and the comparison of the molecular functions of the products of the predicted protein coding genes between A. darlingi and A. gambiae.