We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 Mb and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than 1/3 of Daphnia’s genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The co-expansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes – including many additional loci within sequenced regions that are otherwise devoid of annotations – are the most responsive genes to ecological challenges.

Plants use light as a major source of information for optimizing growth and development. The photoreceptor phytochrome A (phyA) mediates various far-red light induced responses. Here, we show that Arabidopsis FHY3 and FAR1, which encode two proteins related to Mutator-like transposases, act together to modulate phyA signaling by directly activating the transcription of FHY1 and FHL, whose products are essential for light-induced phyA nuclear accumulation and subsequent light responses. FHY3 and FAR1 possess separable DNA-binding and transcriptional activation domains that are highly conserved in Mutator-like transposases. Further, expression of FHY3 and FAR1 is negatively regulated by phyA signaling. We propose that FHY3 and FAR1 define a novel class of transcription factors co-opted from an ancient Mutator-like transposase(s) to modulate phyA signaling homeostasis in higher plants.Plants constantly monitor their light environment in order to grow and develop optimally, using a battery of photoreceptors. Phytochromes are a family of photoreceptors that monitors the incident red (R, 600-700 nm) and far-red (FR, 700-750 nm) light wavelengths by switching reversibly between the R-absorbing, biologically inactive Pr form and the FR-absorbing, biologically active Pfr form (1,2). Upon photoactivation, phyA, the primary photoreceptor for FR light, is translocated from the cytoplasm into the nucleus to induce FR-responsive gene expression required for various photoresponses, such as seed germination, seedling deetiolation, FR-preconditioned blocking of greening, and flowering (3). Genetic studies have identified two pairs of homologous genes essential for phyA signaling: FAR1 (far-red-impaired response 1) and FHY3 (far-red elongated hypocotyl 3); FHY1 (far-red elongated hypocotyl 1) and FHL (FHY1-like) (4-7). FHY1 and FHL have been implicated in mediating the lightdependent nuclear accumulation of phyA (8,9). However, the biochemical function of FHY3 and FAR1 remains to be elucidated. FHY3 and FAR1 share extensive sequence homology with MURA, the transposase encoded by the maize Mutator element, and the predicted transposase of the maize mobile element Jittery (10,11). Both of these transposons are members of the superfamily of Mutator-like elements (MULEs) (12). Database mining and phylogenetic analysis revealed that FHY3/ FAR1-like sequences are present in various angiosperms and fall into several phylogenetic clusters intermingled with MULE transposases (13,table S1 and fig. S1). These proteins share an N-terminal C2H2-type zinc-chelating motif of the WRKY-GCM1 family, a central putative core transposase domain, and a C-terminal SWIM motif (14,15), with highly conserved predicted secondary/tertiary structures ( fig. S2 and S3). To investigate the molecular function

“Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

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 of nematodes that cause lymphatic filariasis. It is one species within the Culex pipiens species complex and enjoys a distribution 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. We describe the genomic sequence of C. quinquefasciatus, its repertoire of 18,883 protein-coding genes is 22% larger than Ae. aegypti and 52% larger than An. gambiae with multiple gene family expansions including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.