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Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics

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Science  01 Oct 2010:
Vol. 330, Issue 6000, pp. 86-88
DOI: 10.1126/science.1191864

Abstract

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.

Mosquitoes are the most important vectors of human disease and are responsible for the transmission of pathogens that cause malaria (Anopheles), yellow fever and dengue (Aedes), as well as lymphatic filariasis and encephalitis viruses (Culex, Aedes, Anopheles). Sequencing the Anopheles gambiae and Aedes aegypti genomes has provided important insights into the genomic diversity underlying the complexity of mosquito biology (1, 2). We describe the sequencing of the Culex quinquefasciatus (the southern house mosquito) genome, which offers a reference genome from the third major taxonomic group of disease-vector mosquitoes. With more than 1200 described species, Culex is the most diverse and geographically widespread of these three mosquito genera. Apart from contributing to the spread of West Nile encephalitis, it also transmits St. Louis encephalitis and other viral diseases and is a major vector of the parasitic Wuchereria bancrofti nematode that has caused the majority of the 120 million current cases of lymphatic filariasis (3).

Taxonomy of the Culex pipiens species complex is the subject of a long-standing debate, an issue complicated by the occurrence of viable species hybrids in many geographic areas [reviewed in (4, 5)]. We followed the standard set by the National Center for Biotechnology Information and refer to the species sequenced here as C. quinquefasciatus. The Johannesburg strain of C. quinquefaciatus was established from a single pond in Johannesburg, South Africa—an area where the two taxa, C. quinquefasciatus and C. pipiens, were found to be sympatric [(5) therein described as subspecies C. pipiens quinquefasciatus and C. pipiens pipiens] but have remained much more genetically distinct than the same two sympatric taxa found in California.

We were able to map 9% of the C. quinquefasciatus genes (1768 genes) on the three chromosomes with the use of published and new C. quinquefasciatus and Ae. aegypti markers (6). Of these mapped genes, 803 had An. gambiae orthologs and 641 had Drosophila melanogaster orthologs, consistent with the established species phylogeny (Fig. 1A). Examining correlations between chromosomal arms indicated whole-chromosome conservation between C. quinquefasciatus, An. gambiae, and D. melanogaster (Fig. 1B) (6), whereas—and as suggested from earlier work (7)—Ae. aegypti appears to have experienced an arm exchange between the two longest chromosomes after the Aedes/Culex divergence (fig. S1).

Fig. 1

(A) Codon-based estimates of DNA substitutions along the mosquito phylogeny: C. quinquefasciatus (Cq), Ae. aegypti (Aa), and An. gambiae (Ag) with D. melanogaster (Dm) as an outgroup. Dates of divergence were taken from previous studies (6). mya, million years ago. (B) Chromosomal synteny between C. quinquefasciatus, Ae. aegypti, An. gambiae, and D. melanogaster. Solid lines indicate main orthologous chromosomes; the dashed line denotes secondary orthologous chromosomes. Colors indicate syntenic chromosome arms. Chromosomes are not drawn to scale. (C) Orthology delineation among the protein-coding gene repertoires of the three sequenced mosquito species. Categories of orthologous groups with members in all three species include single-copy orthologs in each species (1:1:1) and multicopy orthologs in all three (N:N:N), one (N in 1), or two (N in 2) species. Remaining orthologous groups include single or multicopy groups with genes in only two species (X:X:0, X:0:X, 0:X:X). The remaining fractions in each species (Cq/Aa/Ag-specific) exhibit no orthology with genes in the other two mosquitoes.

A significant fraction of the assembled C. quinquefasciatus genome (29%) was composed of transposable elements (TEs) (fig. S2). This amount is less than the TE fraction of Ae. aegypti (42 to 47%), but greater than that of An. gambiae (11 to 16%) (1, 2, 6), suggesting an increased level of TE activity and/or reduced intensity of selection against TE insertions in the two culicinae lineages since their divergence from the An. gambiae lineage. A comparative analysis of the age distribution of the different TE types in the three sequenced mosquito genomes revealed that retrotransposons have consistently been the dominant TE type in the Ae. aegypti lineage over time (fig. S3). More recently, retrotransposons have become the predominant type of TEs active in all three species.

The C. quinquefasciatus repertoire of 18,883 protein-coding genes is 22% larger than that of Ae. aegypti (15,419 genes) and 52% larger than that of An. gambiae (12,457 genes) (Fig. 1C). Our estimated gene number combines ab initio and similarity-based predictions from three independent automated pipelines, optimizing gene identification (6). The relative increase in C. quinquefasciatus gene number is explained in part by the presence of substantially more expanded gene families, including olfactory and gustatory receptors, immune-related genes, and genes with possible xenobiotic detoxification functions (table S1). Expert curation of selected gene families revealed expansions in cytosolic glutathione transferases and a substantial expansion of cytochrome P450s. A large cytochrome P450 repertoire may reflect adaptations to polluted larval habitats and may have played a role in rendering this species particularly adaptable to evasion of insecticide-based control programs, with several C. quinquefasciatus P450s being associated with resistance (8, 9).

Mosquitoes are the subject of intense efforts aimed at designing novel vector control methods that are often based on the ability of the insect to sense its environment (10, 11). C. quinquefasciatus has the largest number of olfactory-receptor–related genes (180) of all dipteran species examined to date (table S1). This expansion may reflect culicine olfactory behavioral diversity, with particular regard to host and oviposition site choice. C. quinquefasciatus females are opportunistic feeders, being able to detect and feed on birds, humans, and livestock, depending on their availability. This plasticity in feeding behavior contributes to the ability of C. quinquefasciatus to vector pathogens, such as West Nile virus and St. Louis encephalitis virus, from birds to humans. The repertoire of gustatory receptors, which are known to mediate perception of both odorants and tastants (12), has also expanded in C. quinquefasciatus, primarily through a large alternatively spliced gene locus.

The saliva of blood-sucking arthropods contains a complex cocktail of pharmacologically active components that disarm host hemostasis (13). The ability of C. quinquefasciatus to feed on birds, humans, and livestock would suggest that it contains an expanded number of proteins that would increase its ability to imbibe blood from multiple host species. Consistent with this idea, a large protein family unique to the Culex genus, the 16.7 kD family, was previously discovered after salivary transcriptome analysis (13). The genome of C. quinquefasciatus revealed 28 additional members of this family.

We have outlined and quantified general similarity and differences at the chromosomal and genomic levels between three disease-vector mosquito genomes, building a foundation for more in-depth future analyses. We found substantial differences in the relative abundance of TE classes among the three mosquitoes with sequenced genomes. Most unexpectedly, this study revealed numerous instances of expansion of C. quinquefasciatus gene families compared with An. gambiae and the more closely related Ae. aegypti. The consequent diversity in many different genes may be an important factor that led to the wide geographic distribution of C. quinquefasciatus.

Supporting Online Material

www.sciencemag.org/cgi/content/full/330/6000/86/DC1

Materials and Methods

Figs. S1 to S12

Tables S1 to S14

References

References and Notes

  1. Materials and methods are available as supporting material on Science Online.
  2. This work was supported by NIH grant HHSN266200400039C and by the National Institute of Allergy and Infectious Diseases, NIH, Department of Health and Human Services under contract numbers N01-AI-30071 and HHSN266200400001C. The assembled genome was deposited in the GenBank database with accession number AAWU00000000.
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