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1 the Black Fly (Diptera: Simuliidae) Genome and EST Project The Black Fly (Diptera: Simuliidae) Genome and EST Project Black Fly Genome Consortium Organizing Laboratories: Marine & Aquatic Genetics, Biology,Creighton University, Omaha, NE. (Brockhouse) Center for Genomics and Biotechnology(CGB), Indiana University, Bloomington, IN. (Cobourne) Department of Entomology, Natural History Museum, London, U.K. (Post) Biodiversity of Medically Important Arthropods Laboratory, Clemson University, Clemson, SC. (Adler) Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana, (Wilson, Boakye) Freshwater Ecology Laboratory, University of South Alabama, Mobile, AL. (McCreadie) Abstract: We propose a full genome sequencing project and an accompanying cDNA sequencing project for the Simuliidae (Black Flies). The full genome sequence will be an invaluable resource for the insect genomics community, that will allow order-wide functional genomic comparative analysis of genomic contents and their organization, as well as functional analyses of critical parameters such as insect attributes linked to their capacity to transmit disease agents. These attributes include blood feeding (haematophagy), parasite/pathogen transmission, symbiosis, and insecticide resistance. The EST project is critical to assembling the full genome in the face of the absence of genetic maps and the presence of inversion polymorphisms, and will enormously enhance efforts to genetically map the black fly genome and explore gene regulation, differences among species, and symbiosis. The cDNA project is a critical component of this proposal, to facilitate the annotation of the genome sequence and to produce reliable microarrays that will be used to explore the conservation of transcriptional regulators under conditions that are shared by species that vector the agents of disease. This project aims to make a significant impact in furthering genomic knowledge of vector biology, by promoting comparative research on a disease vector that has close phylogenetic relationships to both mosquitoes (Anopheles, Aedes) and non-haematophagous insects. Biological material will be supplied by participating laboratories (Noblet, Brockhouse, Adler, Post, McCreadie, Wilson, Boakye), while the CGB will carry out the genomic projects in support of the genome sequencing and effort, including cDNA library construction/screening, sequence assembly validations, EST characterization, and related bioinformatics. The principal investigators will solicit the involvement of a growing insect genomics research community for the overall analysis and annotation. The resulting database will be incorporated into VectorBase and within the proposed InsectBase. 1) Justification for Sequencing the Black Fly Genome. Family Simuliidae: Importance to Humans and the Environment Black flies are generally regarded as the second most pernicious group of insects that afflict the health and economic well-being of humans (Adler et al., 2004). The blood-feeding activity of the adult females transmits a variety of pathogens, notably Onchocerca, Leucocytozoon, Mansonella, Trypanosoma, and Dirofilaria (Adler, 2005) Onchocerca volvulus alone infects approximately 19 million people on two continents, and has been the focus of one of the World Health Organization’s largest programs (Onchocerciasis Control Programme). 1 In spite of these associated pathogens, much of the negative impact of black flies is not due to transmission of disease agents, but to the effects of sheer mass biting. In the northern hemisphere, vast areas are rendered nearly uninhabitable due to the biting rates (Adler et al., 2004). This is also true of developing countries in the tropics, where biting nuisance is recognized as a major barrier to economic development (Huggard et al., 1998). Ironically, while the adult females pose an enormous burden to human well being, the larvae are keystone species in rivers and constitute an essential ecological resource. Black fly larvae are aquatic filter feeders and are able to capture material classified as “dissolved organic matter” (DOM, in ecological parlance). This material is available to few other macroinvertebrates. As a result, this material becomes available to other macroinvertebrates and other organisms which feed either directly on the black flies or on their fecal pellets (Malmqvist, 2004). Despite the medical and ecological importance of black flies, progress on simuliid molecular biology has been slow. This is largely due to the tremendous difficulty in creating and maintaining laboratory colonies. Only one colony of a single species (Simulium vittatum) currently exists at the University of Georgia (Athens). As a consequence, the bulk of work must be conducted using wild-collected material from populations that are highly polymorphic, often of mixed species, and often parasitized or carrying poorly characterized symbionts and pathogens (for review of black fly pathogens see Crosskey, 1990). Black Flies (The Simuliidae): A Window on the Mosquito Genome. Although significant pests in their own right, black flies pale in comparison to mosquitoes as vectors of disease agents, especially with respect to the range of pathogens transmitted. (several of the mosquito-borne pathogens have been listed as bio-terror agents). A great deal of the vectorial capacity of mosquitoes is due to the simple mechanics of blood-feeding: mosquito mouthparts actually travel into the capillaries to imbibe blood, whereas black flies are pool-feeders that slash the skin and lap the oozing blood; pathogens are more directly inoculated into the host by the hypodermic mechanism of mosquitoes than through the lapping action of simuliids (cf. Clements, 1999; Crosskey, 1990). Given the potential number of mosquito species (>3500) available as vectors, it is not feasible to completely sequence all potentially important haematophagous mosquito genomes. By using an appropriate “outgroup” to the three existing mosquito genome projects, however, it is possible to construct a “consensus” view of the mosquito genome. The black fly genome provides the perfect “outgroup” with which to better understand the mosquito genome. Black flies are members of the Culicimorpha, allied to mosquitoes, but separated from them by several other families (Wood and Borkent, 1989). They are taxonomically closer to the culicids than are other dipterans with sequenced genomes (e.g. the drosophilids), and significantly the Culicidae and Simuliidae have startling parallels in their biology, many of which are independently derived. For example, both mosquitoes and simuliids have obligatory aquatic larvae, both groups are female-hematophagous (possibly independently derived; Black and Kondratieff, 2005), and both include members that have secondarily abandoned blood-feeding in either an obligatory or facultative manner. The females of both groups exhibit complex host-seeking behavior involving visual and olfactory cues. The list of parallels continues: insecticide resistance is a significant problem in black flies and mosquitoes, both exhibit inter- and intra-specific variation in vectorial capacity, and both have a propensity for sibling species, which pose great taxonomic and genetic challenges. Parallel development of many of these traits presents a sterling opportunity for genome-wide 2 searches for selection. Selection leaves imprints on the genome (e.g., differential mutation rates between silent and non-silent sites) that allows the detection of genes involved in the processes being examined (e.g., Savard et al., 2006; Steinke et al., 2006). Having the full gene inventories is also useful to detect lineage-specific gene family expansions (or reductions) as a function of the organisms’ biology. By obtaining the fully characterized simuliid genome, rather than just partial sequences or ESTs alone, the wider dipteran and arthropod genomics communities will be able to engage in functional genomic studies, focusing on haematophagy and ecological traits at the family level, for example. 2) No Member of the Simuliidae is Currently the Focus of a Genome Project. In spite of the very early beginnings of black fly molecular biology (Teshima, 1972; Sohn et al., 1975), no black fly genome has been sequenced nor has another proposal been made to sequence a black fly genome to our knowledge. However, a BAC library is currently being prepared from S. squamosum (a member of the S. damnosum complex and a vector of onchocerciasis) by the Post laboratory. This library will be available for the genome sequencing project. 3) Interest to the Scientific Community The community of black fly workers includes representation on all the populated continents, and is represented by three major professional organizations (North American Black Fly 4 Association, British Simuliid Group, and the European Simuliid Symposium Group.) The North American and British groups meet annually, and the European group every two years, with international meetings held periodically (the September 2006 Novi Sad meeting was the 5th such meeting). Approximately 250 laboratories worldwide either focus on simuliids or include black flies as a major part of their research program. Additionally, black flies have been used for comparative purposes by workers concentrating on other taxa, most notably mosquitoes (e.g., Edwards et al., 1997; Pennington et al., 2002) Specific participants from the black fly community include Brockhouse (Creighton University), Adler (Clemson University), McCreadie (University of South Alabama), Post (Natural History
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