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 ϳ16,000 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.

ABSTRACT-Considerable long-standing controversy and confusion surround the phylogenetic affinities of pinnipeds, the largely marine group of "fin-footed" members of the placental mammalian order Carnivora.Until most recently, the two major competing hypotheses were that the pinnipeds have a single (monophyletic) origin from a bear-like ancestor, or that they have a dual (diphyletic) origin, with sea lions (Otariidae) derived from a bear-like ancestor, and seals (Phocidae) derived from an otter-, mustelid-, or musteloid-like ancestor. We examined phylogenetic relationships among 29 species of arctoid carnivorans using a concatenated sequence of 3228 bp from three nuclear loci (apolipoprotein B, APOB; interphotoreceptor retinoid-binding protein, IRBP; recombination-activating gene 1, RAG1 Bayesian inference phylogenetic analyses of separate and combined datasets produced trees with largely congruent topologies. The analyses of the combined dataset resulted in well-resolved and well-supported phylogeny reconstructions. Evidence from nuclear DNA evolution presented here contradicts the two major hypotheses of pinniped relationships and strongly suggests a single origin of the pinnipeds from an arctoid ancestor shared with Musteloidea to the exclusion of Ursidae.

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Exposure to methyl viologen in the presence of light facilitates the production of superoxide that gives severe damage on photosynthetic apparatus as well as many cellular processes in cyanobacteria and plants. The effects of methyl viologen on global gene expression of a unicellular cyanobacterium Synechocystis sp. strain PCC 6803 were determined by DNA microarray. The ORFs sll1621, slr1738, slr0074, slr0075, and slr0589 were significantly induced by treatment of methyl viologen for 15 min commonly under conditions of normal and high light. One of these genes, slr1738, which encodes a ferric uptake repressor (Fur)-type transcriptional regulator, is located divergently next to another induced gene, sll1621, in the genome. We deleted slr1738, and compared the global gene expression patterns of this mutant to that of wild type under non-stressed conditions. It was found that sll1621 was derepressed to the greatest extent, while many other genes including slr0589 but not slr0074 or slr0075 were derepressed to lesser extent in the mutant. Genetic disruption of sll1621, which encodes a putative type 2 peroxiredoxin, indicates that it is essential for aerobic phototrophic growth in both liquid and solid media in high light and on solid medium even in low light. Slr1738 was prepared as a His-tagged recombinant protein and shown to specifically bind to the intergenic region between sll1621 and slr1738. The binding was enhanced by dithiothreitol and abolished by hydrogen peroxide. We concluded that the Fur homolog, Slr1738, plays a regulatory role in the induction of a potent antioxidant gene, sll1621, in response to oxidative stress.

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