Project director: Daphnia Genomics Consortium

A complete sequence of the Daphnia pulex genome will be made available in the year 2004 by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) in collaboration with the Environmental Protection Agency (EPA) and the Daphnia Genomics Consortium (DGC). An important first step is to identify an individual clone, within the D. pulex species complex, with low nucleotide polymorphism for a successful reassembly of genomic scaffolds derived from shotgun sequencing. The chosen clone is Log50 - an individual sampled from a naturally inbred population located witin an ephemeral pond a few meters from the Pacific coast in Oregon. The pond is found north of Florence on the east side of highway 101 at milepost 201 in Douglas County. Sequences from the mitochondrial gene ND5 suggests that Log50 belongs to a cluster of D. pulex, endemic to an area west of the Cascade Mountains, called D. arenata (Figure 1 and 2).

Allozyme and microsatellite genotyping suggests that gene diversity within this populations is ~4%. Of 8 randomly chosen individuals, Log50 possessed the lowest nucleotide heterozygosity (~0.14%) at 17 sequenced loci. From ~5700 bp of sequence, Log50 alleles were polymorphic at 8 sites: 4 nucleotide substitutions among three loci plus 4 insertions or deletions.

Further sequence comparisions suggest that Log50's genome sequence will be a valuable genomic tool applicable to all species within the D. pulex complex. Sequence similarity between Log50 and Marie Lake D. pulicaria (source of the cosmid library and microsatellite markers) ranges between 73-97% for regions matching Genbank database records and 43-88% for non-coding regions (Table 1). As expected, nucleotide composition is consistant between D. pulex and D. pulicaria (Table 2).

Figure 1: Log50's geographical location among sampled regions of the Circumarctic Daphnia pulex species complex.	Figure 2: Genealogy of mitochondrial ND5 gene suggests a 93% similarity between Log50 and Marie Lake D. pulicaria. Image from Biological Journal of the Linnean Society, 1998, 65: 347-365.
Table 1: Log 50's genetic similarity to Marie Lake D. pulicaria at nuclear loci.	Table 2: Log50's nucleotide composition compared to Midwest D. pulex and Marie Lake D. pulicaria.

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