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Crenarchaeota are ubiquitous and abundant microbial constituents of soils, sediments, lakes, and ocean waters. To further describe the cosmopolitan nonthermophilic Crenarchaeota , we analyzed the genome sequence of one representative, the uncultivated sponge symbiont Cenarchaeum symbiosum . C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although they were syntenic, overlapping a- and b-type ribotype genomes harbored significant variability. A single tiling path comprising the dominant a-type genotype was assembled and used to explore the genomic properties of C. symbiosum and its planktonic relatives. Of 2,066 ORFs, 55.6% matched genes with predicted function from previously sequenced genomes. The remaining genes partitioned between functional RNAs (2.4%) and hypotheticals (42%) with limited homology to known functional genes. The latter category included some genes likely involved in the archaeal–sponge symbiotic association. Conversely, 525 C. symbiosum ORFs were most highly similar to sequences from marine environmental genomic surveys, and they apparently represent orthologous genes from free-living planktonic Crenarchaeota . In total, the C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives.

Ciona intestinalis is one of the most extensively studied ascidian species and is of particular phylogenetic importance for studying the molecular mechanisms underlying the origin and evolution of chordates and vertebrates (Cameron et al. 2000; Satoh 2003). In addition to having a basic chordate body plan and a compact genome, ascidians provide a simple experimental system for investigating gene networks involved in pattern formation and cell-fate specification during chordate development (Satoh 1994, 2003; Jeffery 2001; Nishida 2002). As a result of these advantages, many efforts have been made in recent years toward developing genomic resources for C. intestinalis. The C. intestinalis genome has been sequenced using the whole-genome shotgun method (Dehal et al. 2002), and eightfold redundant coverage of the genome using random paired-end sequences was generated at the DOE Joint Genome Institute (JGI). Together with sequence data for nearly 480,000 ESTs and 5647 full-length cDNAs from Kyoto University and the National Institute of Genetics (Japan) (Satou et al. 2002), this has permitted the assembly of 2501 scaffolds longer than 3 kb. A total of 60 Mb, or half the assembly, was reconstructed into 177 scaffolds longer than 190 kb, and more than 85% of the assembled sequence was in 905 scaffolds longer than 20 kb. From these data, it is estimated that ∼160 Mb of the C. intestinalis genome is composed of a euchromatic sequence containing 15,852 protein-coding genes (117 Mb), as well as rDNA repeats and other repetitive sequences (Dehal et al. 2002; http://genome.jgi-psf.org/ciona4/ciona4.home.html). Facilitating the construction of physical maps is the generation of large-insert genomic libraries, which have the advantage of being clone-based. C. intestinalis BAC libraries are readily available (Kobayashi et al. 2002), with 6150 clones already end-sequenced by the National Institute of Genetics (Japan) and reported in the data set of the Ciona draft genome (Dehal et al. 2002). The BAC libraries are available from Kyoto University (http://hoya.zool.kyoto-u.ac.jp/cgi-bin/gbrowse/ci). Together with an additional 148 BAC end sequences (BESs) that were analyzed during the sequencing process, this has generated a set of 12,448 raw sequences (6224 paired BAC end sequences) that are now available in the Ghost database (http://hoya.zool.kyoto-u.ac.jp/cgi-bin/gbrowse/ci). However, the assignment of every BES to scaffolds using a high-stringency assembly program is difficult, because polymorphisms and repeat sequences cause multiple end matches to several different scaffolds (e.g., Vinson et al. 2005). Recently, the genomic sequence for another Ciona species, Ciona savignyi, was made available on the internet (http://www.broad.mit.edu/annotation/ciona/). These data have already made it possible to compare sequences in regulatory regions between the two Ciona species (Johnson et al. 2004; Kusakabe et al. 2004). While this sequence information represents an important and valuable resource, in the absence of a genetic context, the system remains largely inaccessible to genome-wide approaches to answering various biological questions. For example, the draft genome has not yet been mapped onto chromosomes, and the assembly of whole-genome shotgun sequences is still fragmented. C. intestinalis has 28 (n = 14) chromosomes (Colombera and Lazzaretto-Colombera 1978). We previously established a method of two-color fluorescent in situ hybridization (FISH) in Ciona (Shoguchi et al. 2004) and observed that counterstaining of Ciona chromosome preparations with DAPI made it possible to recognize the centromere, although the other banding landmarks were not observed (Shoguchi et al. 2004). We also identified 20 metacentric chromosomes and eight submetacentric or subtelocentric chromosomes in our karyotype analysis of Ciona chromosomes (Shoguchi et al. 2005). The largest pair of metacentric chromosomes was named chromosome 1, while the largest pair of submetacentric/subtelocentric chromosomes was named chromosome 2. However, the small size of the chromosomes (most pairs measuring

The compact genome ofFugu rubripeshas 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 toFugu, 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 betweenFuguand human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.

Enhanced biological phosphorus removal (EBPR) is one of the best-studied microbially mediated industrial processes because of its ecological and economic relevance. Despite this, it is not well understood at the metabolic level. Here we present a metagenomic analysis of two lab-scale EBPR sludges dominated by the uncultured bacterium, "Candidatus Accumulibacter phosphatis." The analysis sheds light on several controversies in EBPR metabolic models and provides hypotheses explaining the dominance of A. phosphatis in this habitat, its lifestyle outside EBPR and probable cultivation requirements. Comparison of the same species from different EBPR sludges highlights recent evolutionary dynamics in the A. phosphatis genome that could be linked to mechanisms for environmental adaptation. In spite of an apparent lack of phylogenetic overlap in the flanking communities of the two sludges studied, common functional themes were found, at least one of them complementary to the inferred metabolism of the dominant organism. The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems.

The approximately 60 species of Phytophthora are all destructive pathogens, causing rots of roots, stems, leaves and fruits of a wide range of agriculturally and ornamentally important plants (1). Some species, such as P. cinnamomi, P. parasitica and P. cactorum, each attack hundreds of different plant host species, whereas others are more restricted. Some of the crops where Phytophthora infections cause the greatest financial losses include potato, soybean, tomato, alfalfa, tobacco, peppers, cucurbits, pineapple, strawberry, raspberry and a wide range of perennial tree crops, especially citrus, avocado, almonds, walnuts, apples and cocoa, and they also heavily affect the ornamental, nursery and forestry industries. The economic damage overall to crops in the United States by Phytophthora species is estimated in the tens of billions of dollars, including the costs of control measures, and worldwide it is many times this amount (1). In the northern midwest of the U.S., P. sojae causes $200 million in annual losses to soybean alone, and worldwide causes around $1-2 billion in losses per year. P. infestans infections resulted in the Irish potato famine last century and continues to be a difficult and worsening problem for potato and tomato growers worldwide, with worldwide costs estimated at $5more » billion per year.« less

The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identiWed in the earlier database (v1.0). Within the v2.1 ‘computational secretome,’ 43% showed no signiWcant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed signiWcant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identiWed in culture Wltrates by mass spectrometry (LS–MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identiWed in carbon-starved cultures. Beyond proteases and M6Pase, 28 speciWc gene products were identiWed including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium’s extracellular enzyme systems. Published by Elsevier Inc.

White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These fungi use extracellular oxidative enzymes that are also able to transform related aromatic compounds found in explosive contaminants, pesticides and toxic waste. We have sequenced the 30-million base-pair genome of Phanerochaete chrysosporium strain RP78 using a whole genome shotgun approach. The P. chrysosporium genome reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay. Analysis of the genome data will enhance our understanding of lignocellulose degradation, a pivotal process in the global carbon cycle, and provide a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching. This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens.

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis . The Ciona genome contains ∼16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona , suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.