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Recurring outbreaks of crown-of-thorns starfish (COTS) severely damage healthy corals in the Western Pacific Ocean. To determine the source of outbreaking COTS larvae and their dispersal routes across the Western Pacific, complete mitochondrial genomes were sequenced from 243 individuals collected in 11 reef regions. Our results indicate that Pacific COTS comprise two major clades, an East-Central Pacific clade (ECP-C) and a Pan-Pacific clade (PP-C). The ECP-C consists of COTS from French Polynesia (FP), Fiji, Vanuatu and the Great Barrier Reef (GBR), and does not appear prone to outbreaks. In contrast, the PP-C, which repeatedly spawns outbreaks, is a large clade comprising COTS from FP, Fiji, Vanuatu, GBR, Papua New Guinea, Vietnam, the Philippines, Japan, Micronesia, and the Marshall Islands. Given the nature of Pacific Ocean currents, the vast area encompassing FP, Fiji, Vanuatu, and the GBR likely supplies larvae for repeated outbreaks, exacerbated by anthropogenic environmental changes, such as eutrophication.

Symbiotic dinoflagellates of the genus Symbiodinium are photosynthetic and unicellular. They possess smaller nuclear genomes than other dinoflagellates and produce structurally specialized, biologically active, secondary metabolites. Polyketide biosynthetic genes of toxic dinoflagellates have been studied extensively using transcriptomic analyses; however, a comparative genomic approach to understand secondary metabolism has been hampered by their large genome sizes. Here, we use a combined genomic and metabolomics approach to investigate the structure and diversification of secondary metabolite genes to understand how chemical diversity arises in three decoded Symbiodinium genomes (A3, B1 and C). Our analyses identify 71 polyketide synthase and 41 non-ribosomal peptide synthetase genes from two newly decoded genomes of clades A3 and C. Additionally, phylogenetic analyses indicate that almost all of the gene families are derived from lineage-specific gene duplications in Symbiodinium clades, suggesting divergence for environmental adaptation. Few metabolic pathways are conserved among the three clades and we detect metabolic similarity only in the recently diverged clades, B1 and C. We establish that secondary metabolism protein architecture guides substrate specificity and that gene duplication and domain shuffling have resulted in diversification of secondary metabolism genes.

Many multicellular organisms rely on symbiotic associations for support of metabolic activity, protection, or energy. Understanding the mechanisms involved in controlling such interactions remains a major challenge. In an unbiased approach we identified key players that control the symbiosis betweenHydra viridissimaand its photobiontChlorellasp. A99. We discovered significant upregulation ofHydragenes encoding a phosphate transporter and glutamine synthetase suggesting regulated nutrition supply between host and symbionts. Interestingly, supplementing the medium with glutamine temporarily supports in vitro growth of the otherwise obligate symbioticChlorella, indicating loss of autonomy and dependence on the host. Genome sequencing ofChlorellaA99 revealed a large number of amino acid transporters and a degenerated nitrate assimilation pathway, presumably as consequence of the adaptation to the host environment. Our observations portray ancient symbiotic interactions as a codependent partnership in which exchange of nutrients appears to be the primary driving force.

The question of how novel structures are created by changing genetic information is one of the most challenging issues in evolutionary biology. It is generally accepted that the morphological features of various multicellular animals are built on a common set of genes. Carroll et al. (2001) and Davidson (2006) proposed that the novel features emerged as a result of altered gene expression patterns. Novel genetic material has also contributed to the evolution of novel structures. Much attention has been focused on gene duplications as a mechanism for the evolution of novel genetic material. Particularly in the case of vertebrate evolution, whole genome duplications that occurred twice in ancestral vertebrates have been regarded as the main force driving the evolution of novel structures (Holland et al. 1994). As an additional mechanism, we focus here on domain shuffling (Chothia et al. 2003; Babushok et al. 2007). Several different molecular mechanisms for domain shuffling have been proposed. Since the domains are often correlated with exon boundaries, exon shuffling is believed to be one of the major forces driving domain shuffling (Liu and Grigoriev 2004). In addition, the introns at the boundaries of domains show a marked excess of symmetrical phase combinations, and, consequently, these domains may be inserted without changing the reading frame of ancestral genes (Kaessmann et al. 2002; Vibranovski et al. 2005). Some other mechanisms might have been involved in domain shuffling, such as the simple fusion of genes and recruitment of mobile elements (Babushok et al. 2007; Ekman et al. 2007). In contrast to thorough investigation of the mechanistic aspects of domain shuffling, the contribution of the new genes created by domain shuffling to the evolution of phenotype has not been sufficiently explored. Because domain shuffling occurs more frequently in metazoan lineages than in unicellular organisms, suggesting that domain shuffling played an important role in the evolution of multicellularity (Patthy 2003; Ekman et al. 2007), we reasoned that domain shuffling also contributed to the elaboration of metazoan body plans. In this study, we comprehensively investigated the domain shuffling events during deuterostome evolution. The complete amphioxus genome sequence provides sufficient deuterostome genomic sequences (Dehal et al. 2002; Sea Urchin Genome Sequencing Consortium 2006; Putnam et al. 2008) to map the domain shuffling events accurately. We listed gene models that were created by domain shuffling in the ancestors of vertebrates, and examined how domain shuffling contributed to the evolution of new genes for vertebrate-specific characteristics. The contribution of domain shuffling was also examined in the evolution of chordates.

Gene regulatory networks consisting of subcircuits of transcription factors and intercellular signaling molecules are key to an understanding of the complex mechanisms of animal development and evolution (Davidson and Erwin 2006). One of the most intensively studied genetic networks is that for the formation of the animal heart. Since the discovery of the “tinman” gene (Bodmer 1993) and its vertebrate homolog, Nkx2.5 (Lyons et al. 1995), many genes have been found to be involved in heart development in a wide range of animals, from insects to mammals. Actually, it is well established that a gene circuit consisting of GATA, Nkx, and Hand is evolutionarily highly conserved. This gene circuit constitutes a “kernel,” which is evolutionarily inflexible and performs essential regulatory functions in building a body part (Davidson and Erwin 2006). Analyses of vertebrate heart development revealed that the differentiation of cardiac muscle cells and morphogenesis of the heart are governed by this heart kernel gene regulatory network (Cripps and Olson 2002; Harvey 2002; Buckingham et al. 2005). An important question to be answered about the formation of the heart in vertebrates and other chordates is how this kernel is turned on at the earliest stages of the heart cell specification process to establish the heart field. Another intriguing question in chordate heart formation is how the dualor multichambered heart of vertebrates evolved. It is generally believed that the ancestral chordate resembled the present-day ascidian tadpole. The morphogenetic movement of heart precursor cells during ascidian larval development and metamorphosis is reminiscent of those in vertebrates (Davidson and Levine 2003). However, the ascidian tube-like heart lacks chambers. The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates. In this issue of Genes & Development, Davidson et al. (2006) addressed these questions by examining the function of an Ets-containing transcription factor in the tunicate, Ciona intestinalis. They found that Ci-Ets1/2 (because this is one of two Ciona orthologs for vertebrate Ets1 and Ets2 and Drosophila pointed, it was originally called Ci-ets/pointed2) (Yagi et al. 2003) establishes the heart field, probably through an FGF signal acting downstream from Ci-Mesp, a basic helix–loop–helix transcription factor gene required for the initial specification of heart precursor cells (Satou et al. 2004). Targeted inhibition of Ci-Ets1/2 or FGF receptor function blocks heart formation. Moreover, targeted expression of a constitutively active Ci-Ets1/2 causes the expansion of the heart field by forced recruitment of larval tail muscle cells that express Ci-Mesp. Interestingly, this heart field expansion, evoked by the subtle alteration of the heart genetic program, caused a morphological change—that is, to a heart with two compartments.

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

Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging for highly polymorphic species. The difficulty arises because two divergent haplotypes are sequenced together, making it difficult to distinguish alleles at the same locus from paralogs at different loci. We present here a method for assembling highly polymorphic diploid genomes that involves assembling the two haplotypes separately and then merging them to obtain a reference sequence. Our method was developed to assemble the genome of the sea squirt Ciona savignyi, which was sequenced to a depth of 12.7× from a single wild individual. By comparing finished clones of the two haplotypes we determined that the sequenced individual had an extremely high heterozygosity rate, averaging 4.6% with significant regional variation and rearrangements at all physical scales. Applied to these data, our method produced a reference assembly covering 157 Mb, with N50 contig and scaffold sizes of 47 kb and 989 kb, respectively. Alignment of ESTs indicates that 88% of loci are present at least once and 81% exactly once in the reference assembly. Our method represented loci in a single copy more reliably and achieved greater contiguity than a conventional whole-genome assembly method.