Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk.

SUMMARYWe explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species-and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.

One key element in understanding the molecular machinery of the cell is to understand the structure and function of each protein encoded in the genome. A very successful means of inferring the structure or function of a previously unannotated protein is via sequence similarity with one or more proteins whose structure or function is already known. Toward this end, we propose a means of representing proteins using pairwise sequence similarity scores. This representation, combined with a discriminative classification algorithm known as the support vector machine (SVM), provides a powerful means of detecting subtle structural and evolutionary relationships among proteins. The algorithm, called SVM-pairwise, when tested on its ability to recognize previously unseen families from the SCOP database, yields significantly better performance than SVM-Fisher, profile HMMs, and PSI-BLAST.

Bacillus subtilis can grow under anaerobic conditions, either with nitrate or nitrite as the electron acceptor or by fermentation. A DNA microarray containing 4,020 genes from this organism was constructed to explore anaerobic gene expression patterns on a genomic scale. When mRNA levels of aerobic and anaerobic cultures during exponential growth were compared, several hundred genes were observed to be induced or repressed under anaerobic conditions. These genes are involved in a variety of cell functions, including carbon metabolism, electron transport, iron uptake, antibiotic production, and stress response. Among the highly induced genes are not only those responsible for nitrate respiration and fermentation but also those of unknown function. Certain groups of genes were specifically regulated during anaerobic growth on nitrite, while others were primarily affected during fermentative growth, indicating a complex regulatory circuitry of anaerobic metabolism.In recent years, Bacillus subtilis has been shown to be a facultative bacterium capable of growing with nitrate or nitrite as the electron acceptor or growing by fermentation in the absence of oxygen (22). The process of dissimilatory reduction of nitrate to ammonia is carried out by two enzymes, the membrane-bound nitrate reductase and the NADH-dependent nitrite reductase (8,9,19). The nitrate reductase is encoded by the narGHJI operon, which is controlled by FNR, an anaerobic regulator (12). The nitrite reductase is encoded by the nasDEF operon, which is not controlled by FNR, since no effect on anaerobic growth on nitrite has been observed in fnr mutant strains. Both fnr and nasDEF regions are regulated by the two-component signal transduction system ResDE, which also controls the expression of the resABC, qcrABC, and cta regions (16,23,28). Furthermore, the ResDE Ϫ mutant requires six-carbon sugars for normal growth. These results indicate that ResDE plays a global role in both aerobic and anaerobic respiration.In the absence of nitrate and nitrite, B. subtilis grows poorly on glucose under anaerobic conditions (18). Efficient fermentative growth can be obtained if pyruvate is provided. Lactates, acetate, and ethanol are found to be the end products of fermentation. Fermentative growth requires the ftsH gene but does not require the FNR gene. In addition, resD and resDE mutations have a moderate effect on fermentative growth. These results suggest that nitrate respiration and fermentation are governed by divergent regulatory pathways (18).Recent advances in functional genomic technologies such as DNA microarray construction provide a unique way to explore the metabolic and genetic control of gene expression on a genomic scale (6). The fact that the complete sequence of B. subtilis is available (14) makes it feasible to apply these functional genomic technologies. To investigate the global changes in gene expression associated with anaerobiosis in B. subtilis, we constructed DNA microarrays containing 4,020 open reading frames (ORFs). These microarrays...