The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.

We analyzed the whole genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors, and identify very rare SNVs. We also directly estimated a human intergeneration mutation rate of ∼1.1×10-8 per position per haploid genome. Both offspring in this family have two recessive disorders--Miller syndrome, for which the gene was concurrently identified, and primary ciliary dyskinesia, for which causative genes have been previously identified. Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the unique value of complete genome sequencing in families.

The complete sequences of Takifugu Toll-like receptor (TLR) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis. Strong selective pressure for recognition of and response to pathogen-associated molecular patterns has maintained a largely unchanging TLR recognition in all vertebrates. There are six major families of vertebrate TLRs. This repertoire is distinct from that of invertebrates. TLRs within a family recognize a general class of pathogen-associated molecular patterns. Most vertebrates have exactly one gene ortholog for each TLR family. The family including TLR1 has more speciesspecific adaptations than other families. A major family including TLR11 is represented in humans only by a pseudogene. Coincidental evolution plays a minor role in TLR evolution. The sequencing phase of this study produced finished genomic sequences for the 12 Takifugu rubripes TLRs. In addition, we have produced >70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt. coincidental evolution ͉ multigene family ͉ concerted evolution T he Toll-like receptor (TLR) multigene family encodes important recognition receptors of the innate immune system that have been conserved in both the invertebrate and vertebrate lineages (1, 2). TLRs recognize a variety of endogenous and exogenous ligands; many of the latter are conserved molecules essential for pathogen survival. TLR genes have been recognized in a number of vertebrate genomes, and many partial and full-length sequences are available. Recent additions include draft predictions from the Japanese pufferfish Takifugu rubripes (3), the zebrafish Danio rerio (4-6), and the chicken Gallus gallus (7), and partially or fully sequenced mRNAs, including one from the goldfish Carassius auratus (8), several from the Japanese flounder Paralichthys olivaceus (9), and several from the rainbow trout Oncorhynchus mykiss (10). These papers provide incremental molecular phylogenetic analyses, and several reviews are available (11-13). Additionally, the draft genomes of the frog Xenopus tropicalis, chicken G. gallus, and opossum Monodelphis domesticus are now available. We present a complete molecular phylogenetic analysis of the known vertebrate TLR genes in the context of the complete genomic sequences of the T. rubripes TLRs. MethodsSequencing and Assembly. A draft genome sequence of T. rubripes was obtained by pairwise shotgun sequencing (14) through the efforts of an international collaboration (15). Sequence finishing was performed in part as described (16), with additional details provided in Supporting Text, which is published as supporting information on the PNAS web site.Bioinformatics. TLRs were identified as genes coding for both an N-terminal leucine-rich repeat (LRR) domain and a C-terminal Toll-IL-resistance (TIR) domain. To form the basis of our study, vertebrate sequences from the nonredundant DDBJ͞EMBL͞ NCBI database (GenBank) were identified by similarity to known TLRs (Data Set 1, which is...

Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis.

De novo mutations (DNMs) originating in gametogenesis are an important source of genetic variation. We use a data set of 7,216 autosomal DNMs with resolved parent of origin from whole-genome sequencing of 816 parent-offspring trios to investigate differences between maternally and paternally derived DNMs and study the underlying mutational mechanisms. Our results show that the number of DNMs in offspring increases not only with paternal age, but also with maternal age, and that some genome regions show enrichment for maternally derived DNMs. We identify parent-of-origin-specific mutation signatures that become more pronounced with increased parental age, pointing to different mutational mechanisms in spermatogenesis and oogenesis. Moreover, we find DNMs that are spatially clustered to have a unique mutational signature with no significant differences between parental alleles, suggesting a different mutational mechanism. Our findings provide insights into the molecular mechanisms that underlie mutagenesis and are relevant to disease and evolution in humans.

Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the TLR-stimulated macrophage undergoes an activation program controlled by a dynamically inducible transcriptional regulatory network. Mapping a complex mammalian transcriptional network poses significant challenges and requires the integration of multiple experimental data types. In this work, we inferred a transcriptional network underlying TLR-stimulated murine macrophage activation. Microarray-based expression profiling and transcription factor binding site motif scanning were used to infer a network of associations between transcription factor genes and clusters of co-expressed target genes. The time-lagged correlation was used to analyze temporal expression data in order to identify potential causal influences in the network. A novel statistical test was developed to assess the significance of the time-lagged correlation. Several associations in the resulting inferred network were validated using targeted ChIP-on-chip experiments. The network incorporates known regulators and gives insight into the transcriptional control of macrophage activation. Our analysis identified a novel regulator (TGIF1) that may have a role in macrophage activation.

The interaction between pathogens and their multicellular hosts is initiated by activation of pathogen recognition receptors (PRRs). These receptors, that include most notably members of the toll-like receptor (TLR) family, recognize specific pathogen-associated molecular patterns (PAMPs). TLR4 is a central part of the receptor complex that is involved in the activation of the immune system by lipopolysaccharide (LPS) through the specific recognition of its endotoxic moiety (Lipid A). This is a critical event that is essential for the immune response to Gram-negative bacteria as well as the etiology of endotoxic shock. Interestingly, compared to mammals, fish are resistant to endotoxic shock. This in vivo resistance concurs with in vitro studies demonstrating significantly lowered sensitivity of fish leukocytes to LPS activation. Further, our in vitro analyses demonstrate that in trout mononuclear phagocytes, LPS fails to induce antiviral genes, an event that occurs downstream of TLR4 and is required for the development of endotoxic shock. Finally, an in silico approach that includes mining of different piscine genomic and EST databases, reveals the presence in fish of all of the major TLR signaling elements except for the molecules specifically involved in TLR4-mediated endotoxin recognition and signaling in mammals. Collectively, our analysis questions the existence of TLR4-mediated cellular responses to LPS in fish. We further speculate that other receptors, in particular beta-2 integrins, may play a primary role in the activation of piscine leukocytes by LPS.

Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system. All data and userfeedback mechanisms are available at the TFCat portal http://www.tfcat.ca. RationaleThe functional properties of cells are determined in large part by the subset of genes that they express in response to physiological, developmental and environmental stimuli. The coordinated regulation of gene transcription, which is critical in maintaining this adaptive capacity of cells, relies on proteins called transcription factors (TFs), which control profiles of gene activity and regulate many different cellular functions by interacting directly with DNA [1,2] and with non-DNA binding accessory proteins [3,4]. While the biochemical properties and regulatory activities of both DNA-binding and accessory TFs have been experimentally characterized and extensively documented (for example, in textbooks devoted to TFs [5,6]), a well-validated and comprehensive catalog of TFs has not been assembled for any mammalian species.Many gene transcription studies have linked the subset of TFs that bind specific DNA sequences to the activation of individual genes and, more recently, these have been pursued on a genome-wide basis using high-throughput laboratory studies (for example, by performing chromatin-immunoprecipitation) as well as computational analyses (for example, by identifying over-represented DNA motifs within promoters of coexpressed genes). To facilitate such efforts, inventories of TFs have been assembled for Drosophila and Caenorhabditis species as well as for specific subfamilies of mammalian TFs