The Genome Sequence of the Malaria Mosquito Anopheles gambiae

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Science  04 Oct 2002:
Vol. 298, Issue 5591, pp. 129-149
DOI: 10.1126/science.1076181

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Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency (“dual haplotypes”) in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.

The mosquito is both an elegant, exquisitely adapted organism and a scourge of humanity. The principal mosquito-borne human illnesses of malaria, filariasis, dengue, and yellow fever are at this time almost exclusively restricted to the tropics. Malaria, the most important parasitic disease in the world, is thought to be responsible for 500 million cases of illness and up to 2.7 million deaths annually, more than 90% of which occur in sub-Saharan Africa (1).

Anopheles gambiae is the major vector of Plasmodium falciparum in Africa and is one of the most efficient malaria vectors in the world. Its blood meals come almost exclusively from humans, its larvae develop in temporary bodies of water produced by human activities (e.g., agricultural irrigation or flooded human or domestic animal footprints), and adults rest primarily in human dwellings. During the 1950s and early 1960s, the World Health Organization (WHO) malaria eradication campaign succeeded in eradicating malaria from Europe and sharply reduced its prevalence in many other parts of the world, primarily through programs that combined mosquito control with antimalarial drugs such as chloroquine. Sub-Saharan Africa, for the most part, did not benefit from the malaria eradication program, but the widespread availability of chloroquine and other affordable antimalarial drugs no doubt helped to control malaria mortality and morbidity. Unfortunately, with the appearance of chloroquine-resistant malaria parasites and the development of resistance of mosquitoes to the insecticides used to control disease transmission, malaria in Africa is again on the rise. Even control programs based on insecticide-impregnated bed nets, now widely advocated by WHO, are threatened by the development of insecticide resistance in A. gambiae and other vectors. New malaria control techniques are urgently needed in sub-Saharan Africa, and to meet this challenge we must grasp both the ecological and molecular complexities of the mosquito. The International Anopheles gambiae Genome Project has been undertaken with the hope that the sequence presented here will serve as a valuable molecular entomology resource, leading ultimately to effective intervention in the transmission of malaria and perhaps other mosquito-borne diseases.

Strain Selection

Populations of A. gambiae sensu stricto are highly structured into several morphologically indistinguishable forms. Paracentric inversions of the right arm of chromosome 2 define five different “cytotypes” or “chromosomal forms” (Mopti, Bamako, Bissau, Forest, and Savanna), and variation in the frequencies of these forms correlates with climatic conditions, vegetation zones, and human domestic environments (2, 3). An alternative classification system based on fixed differences in ribosomal DNA recognizes two “molecular forms” (M and S) (4). The S and M molecular forms were initially observed in the Savanna and Mopti chromosomal forms, respectively. However, analysis of A. gambiaepopulations from many areas of Africa has shown that the molecular and chromosomal forms do not always coincide. This can be explained if it is assumed that inversion arrangements are not directly involved in any reproductive isolating mechanism and therefore do not actually specify different taxonomic units. Indeed, laboratory crossing experiments have failed to show evidence of any premating or postmating reproductive isolation between chromosomal forms (5).

The A. gambiae PEST strain was chosen for this genome project because clones from two different PEST strain BAC (bacterial artificial chromosome) libraries had already been end-sequenced and mapped physically, in situ, to chromosomes. Further, all individuals in the colony have the standard chromosome arrangement without any of the paracentric inversion polymorphisms that are typical of both wild populations and most other colonies (6), and the colony has an X-linked pink eye mutation that can readily be used as an indicator of cross-colony contamination (7). The PEST strain was originally used in the early 1990s to measure the reservoir of mosquito-infective Plasmodium gametocytes in people from western Kenya. The PEST strain was produced by crossing a laboratory strain originating in Nigeria and containing the eye mutation with the offspring of field-collected A. gambiae from the Asembo Bay area of western Kenya, and then reselecting for the pink eye phenotype (8). Outbreeding was repeated three times, yielding a colony whose genetic composition is predominantly derived from the Savanna form of A. gambiae found in western Kenya. This colony, when tested, was fully susceptible to P. falciparum from western Kenya (9). The PEST strain is maintained at the Institut Pasteur (Paris), and A. gambiae strains with various biological features can be obtained from the Malaria Research and Reference Reagent Resource Center (www.malaria.mr4.org).

Sequencing and Assembly

Plasmid and BAC DNA libraries were constructed with stringently size-selected PEST strain DNA. Two BAC libraries were constructed, one (ND-TAM) using DNA from whole adult male and female mosquitoes and the other (ND-1) using DNA from ovaries of PEST females collected about 24 hours after the blood meal (full development of a set of eggs requires ∼48 hours). Plasmid libraries containing inserts of 2.5, 10, and 50 kb were constructed with DNA derived from either 330 male or 430 female mosquitoes. For each sex, several libraries of each insert size class were made, and these were sequenced such that there was approximately equal coverage from male and female mosquitoes in the final data set. DNA extraction, library construction, and DNA sequencing were undertaken by means of standard methods (10–12). Celera, the French National Sequencing Center (Genoscope), and TIGR contributed sequence data that collectively provided 10.2-fold sequence coverage and 103.6-fold clone coverage of the genome, assuming the indicated genome size of 278 million base pairs (Mbp) (tables S1 and S2). Electropherograms have been submitted to the National Center for Biotechnology Information trace repository (www.ncbi.nlm.nih.gov/Traces/trace.cgi) and are publicly available as a searchable data set.

The whole-genome data set was assembled with the Celera assembler (8), which has previously been used to assemble theDrosophila, human, and mouse genomes (12–15). The whole-genome assembly resulted in 8987 scaffolds spanning 278 Mbp of the Anopheles genome (table S2). The largest scaffold was 23.1 Mbp and the largest contig was 0.8 Mbp. Scaffolds are separated by interscaffold gaps that have no physical clones spanning them, although small scaffolds are expected to fit within interscaffold gaps. The sequence that is missing in the intrascaffold gaps is largely composed of (i) short regions that lacked coverage because of random sampling, and (ii) repeat sequences that could not be entirely filled using mate pairs [sequence reads from each end of a plasmid insert (16)]. Most intrascaffold gaps are spanned by 10-kbp clones that have been archived as frozen glycerol stocks. These clones have been submitted to the Malaria Research and Reference Reagent Resource Center (www.malaria.mr4.org). Although there are many scaffolds, 8684 short scaffolds account for only 9% of the sequence data; the remaining 91% of the genome is organized into just 303 large scaffolds.

As the final step of the assembly process, scaffolds were assigned a chromosome location and orientation according to a physical map constructed by in situ hybridization of nearly 2000 PEST strain end-sequenced BACs to salivary gland polytene chromosomes (8). Scaffolds constituting about 84% of the genome have been assigned (table S3), and chromosome arms X, 2L, 2R, 3L, and 3R are represented by 10, 13, 49, 42, and 28 large scaffolds, respectively. Efforts are continuing to map many of the small scaffolds and to increase the density of informative BACs in large scaffolds to approximately one per Mb.

The entire Anopheles genome assembly has been submitted to GenBank. Accession numbers for the 8987 genome scaffolds are AAAB01000001 through AAAB01008987. The entire scaffold set in Fasta format can be downloaded fromftp://ftp.ncbi.nih.gov/genbank/genomes/Anopheles_gambiae/Assembly_scaffolds.

The assembly was screened computationally for contaminating sequence (8) and evaluated for integrity of pairing of mate pairs. Abnormal mate pairs, either with incorrect orientations or with distances that differ from the mean plasmid library insert size by several standard deviations, can be diagnostic of local misassembly. Of 1,644,078 total mate pairs, only 27,703 have distance violations and only 10,166 have orientation violations. However, we identified 726 regions that have high-density mate pair violations (more than six violations per 10 kbp), 639 of which are distance violations with correct orientation. The cause of these violations appears to be separation of divergent genotypes, as discussed below (8). The mean length of these regions is 28 kbp, and in total they constitute 21.3 Mbp or 7.7% of the assembly. These obvious trouble spots have been flagged in our GenBank accessions according to scaffold coordinates and are illustrated as pink bands in Fig. 1.

Figure 1

Assembly of the Y chromosome is ongoing but has been complicated because Y appears to be composed largely of regions containing transposons or transposon fragments that are also found at autosomal centromeres. No scaffolds have yet been assigned to the Y chromosome.

Genetic Variation

Genetic variation within the PEST strain posed a particular challenge to assembling the genome, by making it difficult to distinguish diverged haplotypes from repeats (8). The effect of genetic variation is illustrated in Fig. 2, where correlation among ease of assembly [measured by unitig (17) length], internal consistency of the assembly (measured by mate pair integrity), and genetic variation [measured by single-nucleotide discrepancies (SNDs) (18)] can be clearly seen. The challenges to assembly introduced by this variation exceed those encountered in D. melanogaster or mouse, whose genomes were virtually entirely homozygous, or human, whose genome has a much lower level of polymorphism.

Figure 2

Large-scale correlation of single-nucleotide discrepancies (SNDs) and assembly characteristics over a 10-Mb section from a single scaffold. (A) SND “association” for a sliding window of 100 kb shows the fraction of polymorphic columns whose partitioning is consistent with the partitioning at the previous polymorphic columns (20). (B) SND “balance” for a sliding window of 100 kb compares the ratio of fragments in the second most frequent character in a column to fragments in the most frequent character (19). (C) SND rate shows counts of polymorphic columns in a sliding window of 100 kb (18). (D) Unitig size is shown as the mean size of 21 adjacent unitigs. (E) Mate pair violations are shown by drawing a yellow line segment for each mate pair that is correctly oriented but has its fragments separated by more than three standard deviations from the library mean. A red segment corresponds to each incorrectly oriented mate pair.

The most highly variable regions in the genome appeared to consist of two haplotypes of roughly equal abundance (“dual haplotypes”), as revealed by strong concordance among SND rate, SND balance (19), and SND association (20) (Fig. 2). The most likely explanation is that recombination among the A. gambiae cytotypes that contributed genetically to the PEST strain resulted in a mosaic genome structure. The underlying polymorphic differences between the Savanna and Mopti cytotypes may reflect important differences in their biologies. Two other possible causes for dual haplotypes are the widespread presence of genomic inversions that suppress recombination [as in Drosophila pseudoobscura(21)], and real duplications in the genome that were erroneously collapsed in the assembly.

Details of the assembly make each of these alternative explanations unlikely. First, the PEST strain was specifically selected to lack large, cytologically visible inversions. If its genome still contained numerous small inversion polymorphisms, one would expect the assembly to display a characteristic pattern of mate pair misorientations. For example, suppose that there were a previously undetected inversion that defined the major alleles in a given region, and that the assembly integrated both copies of the inversion into a single contig that was placed in a scaffold also containing the flanking single-haplotype regions. In this situation, mate pairs straddling an inversion breakpoint would include one of the sequenced ends in inverted orientation (fig. S1). Such misorientations were not detected. Second, the collapse of two duplicated regions of the genome as the basis for the observation of dual haplotypes can be similarly dismissed, as this explanation would imply that fragment coverage in the dual-haplotype regions should be approximately twice that of single-haplotype regions. In fact the reverse is true: Fragment coverage tends to be lower in the dual-haplotype regions. A final possibility that remains to be fully tested is a prevalence of balanced lethal mutations. If there were tightly linked balanced lethal alleles in the PEST strain, then all viable individuals would be heterozygous in regions of the genome surrounding the lethal alleles. Sampling of the two alternative haplotypes in the shotgun sequence therefore ought to be binomial with a 50:50 chance of either haplotype. Although haplotypes do appear to be approximately balanced in dual-haplotype regions (Fig. 2), we have been unable to confirm a statistical fit of allele frequency to such a model. A direct test for SNP heterozygosity among individuals of the PEST strain is under way and should resolve the issue of genotypic frequencies in these regions.

Many of the SNDs occurred in regions having small unitigs (17) and other attributes suggesting difficulties with the assembly. Although there is a co-clustering of small unitigs, mate pair violations, and SNDs, not all regions with a high density of SNDs have problematic assemblies. The breeding history of the PEST strain ofA. gambiae (8) led us to predict that the strain would not be totally inbred, which suggested that the genome would also harbor a large number of polymorphic nucleotides (single-nucleotide polymorphisms or SNPs). High-quality discrepancies of base calls in regions where the assembly is strongly supported ought to be considered as SNPs, allowing a genome-wide analysis of polymorphism.

Celera designed and implemented a SNP pipeline for identifying SNPs on the basis of high–sequence quality mismatches in the human whole-genome assembly (8, 12). With some parameter tuning, the same pipeline was adapted to identify SNPs in theAnopheles genome and produced a conservative inference of 444,963 SNPs.

The distribution of SNPs along the chromosomes was highly variable, with some regions having only a few SNPs per 100 kb and others having more than 800 SNPs per 100 kb (Fig. 3), despite a nearly homogeneous power to detect them. The overall estimate of mean heterozygosity at the nucleotide level of this strain is 1.6 × 10−3, but the distribution has high variance and skew, with 45% of the 100-kb intervals having heterozygosity below 5.0 × 10−5 and 10% of the 100-kb intervals having a heterozygosity above 4.7 × 10−2. The X chromosome has a markedly lower average level of polymorphism, and overall the X-linked nucleotide heterozygosity is 1.2 × 10−4, markedly below that of the autosomes (discussed below).

Figure 3

Density of SNPs across the genome of the PEST strain of A. gambiae. The red line indicates the number of inferred SNPs per 100 kb in nonoverlapping windows; the blue line is a running average over 1 Mb. The exceptional regional heterogeneity in SNP density is likely due to the introgression of Mopti and Savanna cytotypes.

It appears that the genome of the PEST strain has resulted from a complex introgression of divergent Mopti and Savanna chromosomal forms (cytotypes). If this is so, then we would expect that some genomic regions may be derived only from one or the other cytotype, yielding a low density of SNPs, whereas other genomic regions may continue to segregate both divergent cytotypes. Microsatellite surveys suggest that the degree of sequence divergence between haplotypes derived from the Mopti and Savanna cytotypes exceeds the variability within each (22), so genomic regions with both cytotypes segregating might be expected to have unusually high SNP density. As predicted by this model, the resulting SNP density distribution is markedly bimodal (Fig. 4), with one mode at roughly one SNP every 10 kb, and another mode at one SNP every 200 bp. SNP rates along the X chromosome for the most part do not show this bimodal pattern; we take this to imply a lower rate of introgression on this chromosome, possibly due to male hemizygosity. Although experimental work is required for confirmation, relative lack of introgression seems the most promising explanation for the lower overall SNP rate in the X chromosome, as compared to population genetic explanations based on smaller effective population size of the X chromosome (23, 24). In addition, heterozygosity of the X chromosome is expected to be depressed because of the selection for homozygosity of the X-linked pink eye mutation.

Figure 4

SNP density on autosomes. The red bars represent X-linked SNPs; the lack of bimodality of X-linked SNPs suggests that there was less successful introgression on the X chromosome.

Because BAC clones provide clear information on the organization of SNPs into haplotypes, analysis of BAC sequences is more informative than a random shotgun for inferring the population history of these regions of high SNP density. Recent BAC-by-BAC sequencing of a 528-kb chromosomal region in the PEST strain identified two alternative haplotypes that differ by 3.3% in sequence and extended for at least 122 kb; reverse-transcription polymerase chain reaction analysis revealed their existence in additional strains, indicating that this phenomenon is not unique to the PEST strain (25).

By aligning the SNP calls with predicted genes (gene prediction results are described below), it was possible to place the SNPs into functional categories on the basis of their predicted propensity to alter gene function (e.g., whether they are in intergenic regions, promoter regions, nonsynonymous coding, introns, etc.). Table 1 shows the total count of each functional class and the estimated heterozygosity for the 444,060 SNPs for which this inference could be made. As was the case for the SNPs in the human genome, the overwhelming majority were in intergenic regions, but there was still an abundance of SNPs within functional genes. Introns and intergenic regions had virtually identical heterozygosities, but the silent coding positions appear to have more than twofold enrichment of variability. In general, silent coding sites are considered as having more stringent constraints than introns or intergenic regions because of biased codon usage, and this is reflected in a lower diversity of silent sites in most organisms. The reason for elevated silent variation in A. gambiae is at present unknown. Nucleotides with strong functional constraints, such as splice donors, splice acceptors, and stop codons, had the lowest heterozygosity, and nonsynonymous (missense) positions were also evidently low in heterozygosity. All A. gambiae SNP data discussed here are available atftp://ftp.ncbi.nih.gov/genomes/Anopheles_gambiae/SNP.

Table 1

Distribution of SNPs in the A. gambiaegenome, and their characteristics and heterozygosity per category.

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Automated annotation pipelines established by Celera and the Ensembl group at the European Bioinformatics Institute/Sanger Institute were used to detect genes in the assembled A. gambiaesequence. Both pipelines use ab initio gene-finding algorithms and rely heavily on diverse homology evidence to predict gene structures (8).

We manufactured a “consensus set” of Celera (“Otto”) and Ensembl annotations by first populating a graph wherein each node represented an annotated transcript. For each set, an edge was placed between two transcripts if any of their exons overlapped. By this procedure we found that the 9896 transcripts annotated by Ensembl reduced to 7465 distinct genes, and that the 14,564 Otto transcripts reduced to 14,332 distinct genes. Combining the 9896 Ensembl and 14,564 Otto annotations and subjecting them to the same procedure collapsed the combined 24,460 transcripts to 15,189 genes. Of these, 1375 genes were represented solely by Ensembl and 7840 genes solely by an Otto annotation; 5974 genes were identified by both Ensembl and Otto. We then chose the annotation containing the largest number of exons to represent each gene. In cases where a gene was represented by Otto and Ensembl annotations with equal numbers of exons, we chose the Otto annotation to represent the gene. Results of annotation of the A. gambiae genome are presented in Fig. 1 and Table 2.

Table 2

Features of A. gambiae chromosome arms. Known and unknown genes are defined as genes with an assigned versus unassigned/unclassified GO molecular function. Gaps between scaffolds are included in the chromosome length estimate. Each gap has the arbitrary value of 317,904 bp, which is the total length of the unmapped scaffolds divided by the number of mapped scaffolds. There are 602 known genes, 1017 unknown genes, and 22,123 SNPs on unmapped scaffolds.

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We screened the 15,189 Anopheles gene predictions for transposable element sequences that may not have been adequately masked during the automated annotation process. We also screened for contaminating bacterial gene predictions because the genomic libraries used for sequencing were constructed from whole adult mosquitoes and some level of sequence contamination from commensal gut bacteria was expected. We found 1506 putative transposable elements and 663 genes of possible bacterial origin (8). Analysis of transposable elements in A. gambiae is ongoing, and experimental efforts are currently under way to further characterize bacterial contaminants and to explore the possibility of real horizontal transfer events. Putative transposable elements and bacterial contaminants were flagged before submission to GenBank and, where appropriate, were excluded from further genome analysis either before an automated analysis step was run or during manual interpretation of results.

As a more rigorous quality assurance exercise, we randomly selected 100 annotations from the unflagged portion of the consensus set to manually assess the accuracy of the predicted gene structures. Of these, 35 were predicted correctly, 40 were incompletely annotated (they lacked start and/or stop codons), 4 were merged, 1 was split, and 4 were identified as transposable elements that escaped earlier detection. A further 16 annotations presented various problems with gene structure and needed exon edge adjustment. The large proportion of partial annotations is likely due to lower sequence conservation in gene termini and thus a reduced likelihood of recognition of these regions by similarity-based automated annotation systems.

To estimate the number of genes that may have been missed by the automated annotation process, we examined FgenesH and Grailexp predictions that showed similarity to known proteins but were not represented in the consensus set. We also examined regions where anA. gambiae expressed sequence tag (EST) matched the genomic sequence across a putative splice junction and no gene call was made. On the basis of these analyses, we expect that as many as 1029 genes may have escaped automated annotation and therefore are not displayed in Fig. 1 or included in our analysis of the proteome. TheAnopheles annotation described herein should be considered a first approximation, providing a framework for future improvement by manual curation.

Features of the Genome Landscape

The sizes of the Anopheles and Drosophilagenomes have been predicted by CoT analysis to be 260 Mb (26) and 170 Mb (27), respectively, and the sizes of their genome assemblies are 278 Mb and 122 Mb (13). The discrepancy between estimated and assembled genome size inDrosophila is thought to be due to the nature ofDrosophila heterochromatin, which consists of long tandem arrays of simple repeats that cannot be readily cloned and sequenced with existing technology (13). RegardingAnopheles, there are several immediate possibilities as to why the assembly is slightly larger than the predicted genome size. The CoT analysis could be slightly inaccurate, or, because it was done with DNA of a different strain, the estimate could simply reflect a real strain difference in genome size. In addition, we know that segregation of haplotypes during the assembly process has led to overrepresentation of the size of the genome by about 21.3 Mb (8), and it appears that the Anopheles assembly has captured much of the heterochromatic DNA. Unlike Drosophila, genomic DNA fromAnopheles does not show a prominent heterochromatic satellite band when separated on a cesium chloride gradient (28), which suggests that the heterochromatin is of higher complexity and thus more amenable to sequencing and assembly. In fact, in the Anopheles assembly, there are many scaffolds that exist entirely within known heterochromatic regions or extend into centromeres.

The difference in absolute genome size betweenAnopheles and Drosophila could be due to gain inAnopheles, loss in Drosophila, or some combination thereof. Given that the numbers of genes, numbers of exons, and total coding lengths vary by less than 20% (Table 3), the size difference between the two genomes is due largely to intergenic DNA. The exact nature ofAnopheles intergenic DNA is unclear, but as discussed above, much of it may consist of moderately complex heterochromatic sequence. By counting the number of times each 20-nucleotide oligomer in theAnopheles and Drosophila assemblies appeared in its corresponding whole-genome shotgun data, we confirmed that simple repeats are not expanded in Anopheles (8). However, there does appear to be greater representation of transposons in Anopheles heterochromatin than in Drosophilaheterochromatin, as discussed below.

Table 3

Characteristics of the A. gambiae genome. Fractions of total genome size are shown in parentheses.

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A likely explanation for the size difference of the two genomes is that D. melanogaster has lost noncoding sequence during divergence from A. gambiae. All mosquitoes in the Culicidae family have larger genomes, with estimates of 240 to 290 Mb for Anopheles species and 500 Mb or larger for all others.Drosophila species groups other than D. melanogaster and D. hydei have genomes of 230 Mb or larger (Center for Biological Sequence Analysis, Database of Genome Sizes, www.cbs.dtu.dk/databases/DOGS). This suggests that the two clusters with smaller genome sizes experienced genome reductions during recent evolutionary time. The fact that most other families of the dipteran order have species with genomes at least as large as that ofA. gambiae further supports this conjecture. Mechanisms for this relatively rapid loss of noncoding DNA have been modeled and analyzed in insect species (29, 30).

About 40 different types of transposons or transposon-related dispersed repeats have been identified in the A. gambiaegenome (8) (Table 4). The most abundant are class I repeats, particularly the long terminal repeat (LTR) retrotransposons, small interspersed repeat elements (SINEs), and miniature inverted repeat transposable elements (MITEs), but all major families of class II transposons are also represented. Overall, transposable elements constitute about 16% of the eukaryotic component and more than 60% of the heterochromatic component of the A. gambiae genome (8), as compared to 2% and 8%, respectively, for D. melanogaster (31). Transposons present in heterochromatin are highly fragmented inA. gambiae, so 60% is likely an underestimate. Because heterochromatin appears to be largely derived from transposons, there must be a mechanism that promotes transposon loss from these regions at a rate that balances the insertion of new copies.

Table 4

Repetitive DNA sequences in A. gambiae. Elements are identified by a name already in use in A. gambiae, by the most similar element in another species [usuallyD. melanogaster (-lk = like)], or by commonly recognized family designators (e.g., mariner, piggyBac, or hAT family elements).

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Within the euchromatic part of the genome, repeat density is highest near the centromeres, lowest in the middle of chromosome arms, and somewhat elevated near the telomeres. Moreover, transposon densities differ by arm. Transposon density is highest on the X chromosome (59 transposons per Mb), with chromosome arms 2R, 2L, 3R, and 3L having 37, 46, 47, and 48 transposons per Mb, respectively. Transposon distribution is consistent with the hypothesis that densities are highest in parts of the genome where recombination rates are lowest. The observation that 2R has the lowest overall repeat density may be related to the large number of paracentric inversions on this arm whose frequencies are known to be associated with population structuring (32).

A protein-based method developed to identify genomic duplications (15) was modified to search for segmental chromosomal duplications in the A. gambiae genome. Briefly, at least three proteins within a small interval along a chromosome were required to align with three homologous proteins on a separate genomic interval in order to be considered a potential duplication segment (33). A total of 102 duplication blocks, containing 706 gene pairs, were identified by this method.

We detected only a few large duplicated segments that contain paralogous expansions of a single family distributed in two distinct blocks in the Anopheles genome. These could be the result of a single or limited number of gene duplications to a distinct second chromosomal site, followed by further local tandem duplications at the two sites. Alternatively, such distributions could result from a tandem duplication of a given gene, followed by segmental duplication of the tandem block of paralogous genes. These possibilities can only be distinguished by extensive phylogenetic analyses, and we therefore analyzed the 21 largest tandem cluster pairs in relation toDrosophila. Figure S3 illustrates an example in the glutathione S-transferase gene family. The absence of clear segregation of the Drosophila and Anopheles members, along with other suggestive features of the tree structure, is consistent with tandem gene duplications in the Anopheles/Drosophilacommon ancestor followed by segmental duplication afterAnopheles/Drosophila divergence.

These results should be contrasted with results from other animal genomes. Although the Caenorhabditis elegans (worm) andFugu rubripes (pufferfish) genomes showed minimal evidence of block duplications (34, 35), there was a markedly higher frequency of segmental duplications observed in the human and mouse genomes. Analysis of the human protein set revealed 1077 duplicated blocks containing 10,310 gene pairs, including some blocks encompassing >200 genes (12). Thus, the human analysis revealed more than 10 times the number of potential segmental duplication blocks found in the mosquito, despite a proteome that is only about twice as large. Many of these duplications were mirrored in the mouse genome (15). This contrasts greatly with the observed paucity of segmental duplications in Anopheles; moreover, these duplications are not clearly discernible inDrosophila (36). Thus, the large segmental and chromosome-sized duplications described in vertebrate genomes are not observed in the two insect genomes examined. However, given the limitations of the methods used, ancient large segmental duplications that subsequently underwent massive rearrangement (“scrambling”) would not be detected in this analysis.

A broader comparison of the entire predicted protein sets of A. gambiae and D. melanogaster revealed clear relationships across chromosomes in the two genomes, and in most cases indicated a one-to-one relationship between proteins across the two species. Chromosome 2 of Anopheles shares a common ancestor with chromosome 3 of Drosophila, and chromosome 3 ofAnopheles has a common ancestor—with the left and right arms reversed—with chromosome 2 of Drosophila. More details of this comparison are given in a companion article (37).

The A. gambiae Proteome

Two broad questions were asked: (i) What are the most represented molecular functions of the predicted gene products in A. gambiae, and how do these compare with other sequenced eukaryotic species and the closest sequenced evolutionary neighbor,D. melanogaster? [Our approach involved analysis at the level of protein domains using the InterPro database (38,39) and clustering protein families using a previously published algorithm called LeK (12, 40).] (ii) What are the prominent genes in Anopheles that are associated with blood feeding? In a companion article, specific differences betweenAnopheles and Drosophila genes are examined further, including complementary analyses of strict orthology (Anopheles genes with one clearly identifiable counterpart in Drosophila, and vice versa), microsynteny, and dynamics of gene structure (37).

The results presented here are preliminary, as the gene predictions and functional assignments were computationally generated, and we expect both false-positive predictions (pseudogenes, bacterial contaminants, and transposons) and false-negative predictions (Anopheles genes that were not computationally predicted). We also expect a few errors in delimiting the boundaries of exons and genes. Similar limitations are likely in the automatic functional assignments.

We used InterPro and Gene Ontology (GO) (41) to classify the predicted Anopheles protein set on the basis of protein domains and their functional categories. Figure 1 provides an overview of protein functional predictions according to broad GO molecular function categories, as well as the genomic coordinates of these proteins on mapped scaffolds. We then defined the 50 most prominent InterPro signatures in Anopheles and the representation of these domains in other completely sequenced eukaryotic genomes (table S4). The relative abundance of the majority of proteins containing InterPro domains was similar between the mosquito and fly, with insect-specific cuticle and chitin-binding peritrophin A domains and the insect-specific olfactory receptors being similarly overrepresented. However, there are several classes of proteins that contain domains that are overrepresented in mosquito compared to fly, and comparison of the representation of these domains in other organisms (table S4) suggests that the representational difference is due to expansion in Anopheles rather than loss in Drosophila.

The serine proteases, central effectors of innate immunity and other proteolytic processes (42, 43), are well represented in both insect genomes, but Anopheles has nearly 100 additional members. The presence of additional members in Anopheles is perhaps reflective of differences in feeding behavior and its intimate interactions with both vertebrates and parasites.

We observed expansions of specific extracellular adhesion domain–containing proteins in Anopheles. There are 36 more fibrinogen domain–containing proteins and 24 more cadherin domain–containing proteins in Anopheles than inDrosophila. The fibrinogen domain–containing proteins are similar to ficolins, which represent animal carbohydrate-binding lectins that participate in the first line of defense against pathogens by activating the complement pathway in association with serine proteases (44). As discussed below, several of these members were up-regulated in response to blood feeding. Expansion of cadherin domain–containing proteins is of interest given their prominent role in cell-cell adhesion in the context of morphogenesis and cytoskeletal and visual organization (45, 46). The observed differential expression of some of the members of this family with blood feeding may suggest an unexplored role in regulating the cytoskeletal changes in the mosquito gut to accommodate a blood bolus.

Finally, although there is relative conservation of most of the transcription factor proteins between the two insect genomes and other sequenced organisms (for example, the C2H2 zinc finger, POZ, Myb-like, basic helix-loop-helix, and homeodomain-containing proteins), we observed overrepresentation of the MYND domain–containing nuclear proteins in mosquito. This protein interaction module is predominantly found in chromatinic proteins and is believed to mediate transcriptional repression (47).

Building on a previously published procedure, we used the graph-theoretic algorithm LeK (15, 40) to simultaneously cluster the protein complements of Anopheles andDrosophila. Unlike the above InterPro analysis, which grouped proteins on the basis of domain content, LeK sorted homologous proteins (orthologs plus paralogs) into clusters on the basis of sequence similarity (8). The variance of each organism's contribution to each cluster was calculated, allowing an assessment of the relative importance of organism-specific expansion and contraction of protein families that have occurred since divergence from their common dipteran ancestor about 250 million years ago (48).

The striking degree of evolutionary relatedness betweenAnopheles and Drosophila is illustrated in Fig. 5, with a sizable proportion of theAnopheles proteome represented by clusters with a 1:1 Drosophila ratio. Although there is substantial conservation between Anopheles andDrosophila, the LeK method of analysis provided 483 clusters that contain only Anopheles proteins. Prominent among these is a 19-member odorant receptor family that is entirely absent inDrosophila. It is tempting to speculate that this family may be important in mosquito-specific behavior that includes host seeking.

Figure 5

(A) Relative expansions of protein families in A. gambiae compared to D. melanogaster. The predicted protein sets of Anophelesand Drosophila were subjected to LeK clustering. The numbers of clusters with varying ratios were plotted (numbers ofAnopheles proteins are shown in parentheses). Ranges included for each ratio: 1:1 (0.5 to 1.49), 2:1 (1.5 to 2.49), 3:1 (2.5 to 3.49), 4:1 (3.5 to 4.49), and 5:1 (4.5 to 5.49). (B) Distribution of the molecular functions of proteins represented in LeK clusters with varyingAnopheles:Drosophila ratios. Each slice represents the assignment to molecular function categories in the GO.

To illustrate some of these prominent differences between the two species, we analyzed protein family clusters that showed at least 50% overrepresentation in Anopheles. The degree of overrepresentation and the molecular functions of these proteins are shown in Fig. 5B. In exploring the possible biological relevance of these observed representational differences, we have focused on families with prominent physiological roles (Table 5). These include critical components of the visual system, structural components of the cell adhesion and contractile machinery, and energy-generating glycolytic enzymes that are required for active food seeking. Increased numbers of salivary gland components and anabolic and catabolic enzymes involved in protein and lipid metabolism are consistent with theAnopheles blood feeding and oviposition cycle, described below. Of equal interest are protein families that may play a protective role in Anopheles. These include determinants of insecticide resistance such as transporters and detoxification enzymes. Although the greater numbers of serine proteases have been described previously in the text and table S4, additional differences (seen here in α2-macroglobulin and hemocyanins) are consistent with a complex innate immune system in Anopheles. Finally, representative examples of greater numbers of genes involved in nuclear regulation and signal transduction provide the first glimpse into what perhaps defines a hematophagous dipteran.

Table 5

Representative protein family expansions in A. gambiae, as derived from LeK analysis. A/D ratio,Anopheles/Drosophila ratio.

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After metamorphosis into an adult mosquito, female anopheline mosquitoes take sugar meals to maintain basal metabolism and to energize flight. Flight is needed for mating and finding a host that will provide a blood meal source. The blood meal is a protein-rich diet that the mosquito surrounds after ingestion with the peritrophic matrix (PM), a thin structure containing chitin and proteins. Digestion requires secreted proteases that penetrate the PM. The smaller digestion products are hydrolyzed by microvilli-bound enzymes before absorption by the midgut cells. The blood meal–derived nutrients are processed by the insect fat body (equivalent of the liver and adipose tissue of vertebrates) into egg proteins (vitellogenins) and various lipids associated with lipoproteins. These are exported through the hemolymph to the insect ovaries, where the oocytes develop. The egg development process takes 2 to 3 days, and no further food intake is needed until after oviposition, when a new cycle of active host finding and blood feeding, digestion, and egg development begins (49).

We performed an EST-based screen for genes that are regulated differentially in adult female mosquitoes in response to a blood meal (8). From a starting set of 82,926 ESTs (43,174 from blood-fed mosquitoes, 39,752 from non–blood-fed mosquitoes), we identified 6910 gene loci with at least one EST hit. Using a binomial distribution and a stringent P-value cutoff of 0.001, we identified 97 up-regulated transcripts and 71 that were down-regulated in the blood-fed group (Fig. 6) (table S5). These results are consistent with earlier microarray experiments based on much smaller gene sets (50).

Figure 6

Functional classes of genes corresponding to ESTs from blood-fed and non–blood-fed A. gambiae. The genes that contribute to each functional category are listed in table S5.

After a blood meal, several genes associated with cellular and nuclear signaling, digestive processes, ammonia excretion, lipid synthesis and transport, and translational machinery were overexpressed. In addition, lysosomal enzymes (including proteases found in the fat body and oocytes), genes coding for yolk and oocyte proteins, and genes associated with egg melanization were up-regulated. Conversely, there was down-regulation of genes associated with muscle processes (cytoskeletal and muscle contractile machinery, glycolysis, and ion adenosine triphosphatases) and their associated mitochondrial proteins. Salivary and midgut glycosidases, needed for digestion of a sugar meal, were down-regulated by blood feeding. Four proteins associated with the vision process were also down-regulated, suggesting a degree of detachment of the mosquito from its environment during digestion of a blood meal. Signaling serine proteases of the midgut (important for detection of a protein meal in the gut), peritrophic matrix proteins (matrix components synthesized before the blood meal and accumulated in midgut cell granules), and structural components of the insect cuticle all showed decreased expression after the blood meal. Interestingly, a protein associated with circadian cycle, stress, and feeding behavior was also down-regulated. Finally, the blood meal increased expression of the mitochondrial NADPH-dependent isocitrate dehydrogenase and concomitantly decreased expression of the NAD-dependent form (where NAD is the oxidized form of nicotinamide adenine dinucleotide and NADPH is the reduced form of NAD phosphate). This likely reflects a shift from muscle to fat body metabolism.

Concluding Remarks

Foremost in our minds is how the genomic and EST data can be used to improve control of malaria in the coming decades. Three issues are central to efforts aimed at reducing malaria transmission: reducing the numbers and longevity of infectious mosquitoes, understanding what attracts them to human (as opposed to animal) hosts, and reducing the capacity of parasites to fully develop within them.

Reducing the number of mosquitoes: Anopheline mosquitoes rapidly develop resistance to pesticides. The molecular targets of the major classes of insecticides are known, and mutation of target sites is well understood as a mechanism of resistance (51). However, the molecular basis of metabolic resistance is less clear. The Anopheles genome provides a near-complete catalog of enzyme families that play an important role in the catabolism of xenobiotics (52). Furthermore, the availability of SNPs in these genes will facilitate monitoring of the frequency and spread of resistance alleles and efforts to locate the major loci associated with resistance to DDT and pyrethroids (51,53).

The hematophagous appetite of the female mosquito is exemplified by its remarkable ability to ingest up to four times its own weight in blood. The genome-wide EST expression analysis described here provides evidence that a blood meal results in up-regulation of genes for protein and lipid metabolism, with concomitant down-regulation of genes specific to the musculature and sensory organs. This metabolic reprogramming offers multiple points for intervention. Identification of key pathways that facilitate ingestion of a blood meal provides an opportunity to disrupt the carefully orchestrated host-seeking and concomitant metabolic signals through high-affinity substrate analogs, or by disrupting insect-specific cell signaling pathways.

Reducing the anthropophilicity of the mosquito: The molecular basis for the distinct preference for human blood and the ability to find it is unknown, but it almost certainly involves recognition of human-specific odors. A. gambiae odorant receptors described here and in a companion report (54) may provide insights into what underlies human host preference. This knowledge should be of use in designing safe and effective repellents that reduce the transmission rate of malaria simply by reducing the efficiency with which mosquitoes find and feed on their human prey.

Reducing the development of the malarial parasite:The complex orchestration of the Plasmodium life cycle in Anopheles illustrates several critical points of intervention, such as fusion of gametocytes in the mosquito midgut, penetration of the peritrophic matrix by the ookinete, and migration of sporozooites to the mosquito salivary glands. Likewise, an improved understanding of the Anopheles immune response to the parasite can be exploited to disrupt transmission (55,56). Several recent genomic approaches have provided catalogs of genes involved in the response to a wide range of immune stimuli, including infection by Plasmodium species (43, 50, 55, 56). These strategies provide candidate genes to complement recent developments in generating genetically transformed A. gambiae strains that are refractory toPlasmodium (57–59). Germline transformation thus holds much promise for producing immune-competent, pesticide-susceptible, or zoophilic A. gambiae. However, there are serious complicating factors that must be overcome. Knowing the sequence of the A. gambiae genome will enable further characterization of candidate genes useful for malarial control, and will allow the characterization of mobile genetic elements that may be used for transformation.

Supporting Online Material


Materials and Methods

Figs. S1 to S3

Tables S1 to S5

  • * Present address: Canada's Michael Smith Genome Science Centre, British Columbia Cancer Agency, Room 3427, 600 West 10th Avenue, Vancouver, British Columbia V5Z 4E6, Canada.

  • Present address: Agencourt Bioscience Corporation, 100 Cummings Center, Suite 107J, Beverly, MA 01915, USA.

  • § Present address: Department of Pharmacology, Sun Yat-Sen Medical School, Sun Yat-Sen University #74, Zhongshan 2nd Road, Guangzhou (Canton), 510089, P. R. China.

  • || Present address: Sanaria, 308 Argosy Drive, Gaithersburg, MD 20878, USA.

  • To whom correspondence should be addressed. E-mail: robert.holt{at}celera.com, rholt{at}bcgsc.ca (R.A.H.), frank.h.collins.75{at}nd.edu (F.H.C.).


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