Aspergillus niger Citric acid production by the filamentous ascomycete fungus, Aspergillus niger represents the most efficient, highest yielding bioprocess in practice. This process is a model for other filamentous fungal fermentation processes that will become a key part of DOE's vision of the biorefinery, where multiple products such as organic acids and ethanol, are produced from renewable biomass. These products can be further refined for use as plastic monomers, solvents, or fuels, thereby decreasing dependence on petroleum, the traditional source of these products.

Aureococcus anophagefferens The Aureococcus genome will be the first sequenced for any Harmful Algal Bloom (HAB) species. HABs are blooms of phytoplankton cells resulting in conditions that are unhealthy for humans, animals or ecosystems causing by decrease in light attenuation or oxygen levels, or by production of toxins. HABs may cause marine life poisoning and/or death. Through analysis of the Aureococcus genome, we hope to glean information regarding mechanisms involved in HAB bloom formation and cessation.

Batrachochytrium dendrobatidis is a unique fungus responsible for chytridiomycosis, an emerging infectious disease that is responsible for global amphibian declines. First identified in 1998 on frogs originating from Australia and Central America, B. dendrobatidis has now been reported to be killing frogs on every continent except Asia and Antarctica. The genome sequence of B. dendrobatidis will facilitate studies of its pathogenicity and its epidemiology.

Branchiostoma floridae The Florida lancelet Branchiostoma floridae is a representative of the invertebrate subphylum Cephalochordata. Lancelets, along with tunicates, are members of the chordate phylum, and share the same basic body plan as vertebrates. However, they have a simpler anatomy and physiology than vertebrates, with fewer distinct tissue types and organs. Anatomical, embryological and molecular genetic comparisons between the lancelet and the vertebrates continue to shed light on the evolutionary origin of vertebrates.

Capitella sp. I is a polychaete worm and a representative member of the phylum Annelida, also known as the segmented worms. The Capitella genome sequence complements current developmental and environmental research programs and will provide opportunities to understand genome evolution and its role in body plan and life history evolution in the Metazoa.

Chlamydomonas reinhardtii is a single celled chlorophyte. Highly adaptable, these green algae live in many different environments throughout the world. Normally deriving energy from photosynthesis, with an alternative carbon source, C. reinhardtii can also thrive in total darkness. The relative adaptability and quick generation time has made Chlamydomonas an important model for biological research. Over the years, studies of Chlamydomonas have provided major research contributions in the areas of photosynthesis and molecular biology

Chlorella sp. NC64A is a microalgae of special interest as the host for a family of large plaque-forming dsDNA viruses (called chlorella viruses) that are found in freshwater throughout the world. The NC64A-virus system is a model system for studying DNA virus/algal interactions.

Ciona intestinalis has the smallest genome of any experimentally manipulable chordate. This organism provides a good system for exploring the evolutionary origins of the chordate lineage, from which all vertebrates sprouted. C. intestinalis has a good genomic infrastructure (EST and cDNA collections, BAC and cosmid libraries, etc.), easily visualized cells and morphogenetic processes, existing methods for transient transgene expressions, and is available throughout the world all year long. In addition, there is a deep classical literature on ascidian development, and an active community of researchers worldwide.

Cochliobolus heterostrophus C5 is a natural pathogen of corn, and can be found in many tropical and subtropical areas of the world. In the US, the fungus is usually found in the warmer southern states, thus, the disease it causes is commonly known as Southern Corn Leaf Blight (SCLB). Although species of Cochliobolus are not, currently, among the most economically serious diseases, they have proven their ability to cause extraordinary crop losses. As cereal crops mature as a source of biomass for biofuel and bioproduct production, factors that lower crop yield become even more economically important.

Daphnia pulex The globally distributed zooplankton Daphnia (commonly called the waterflea) is the first crustacean to have its genome sequenced. Daphnia has fascinated biologists for centuries because of its importance in aquatic ecosystems, its amenability to both field and laboratory study, and because of its remarkable ability and flexibility to cope with environmental challenges.

Dictyostelium purpureum QSDP1 Modern molecular phylogenetic evidence points to a wide diversity of simple eukaryotes, diverging at various points along the tree of life. The amoebozoa form part of a supergroup of eukaryotes that form a sister clade to the fungi and animals, having diverged more recently than the plants. Among the amoebozoa are the social amoebas or the dictyostelids, which exhibit the characteristic behavior of forming multicellular organisms under certain growth conditions. The dictyostelids actually comprise four major phylogenetic groups, representing evolutionary forms as diverse as the animal kingdom.

Emiliania huxleyi CCMP1516 is the most prominent coccolithophore and has attracted the attention of scientists from fields as diverse as geology, biogeography, paleoclimatology, ecophysiology, material science, and medicine. E. huxleyi is distributed throughout the world’s oceans and is linked to the chemical balance between the atmosphere, hydrosphere, and geosphere. Massive blooms of the algae can cover 100,000s of square kilometers and can be detected via satellite imagery due to the reflective properties of its coccoliths.

Fugu (Takifugu) rubripes has the shortest known genome of any vertebrate species. As vertebrates, fish and humans share not only the defining characteristic of a backbone, but also many basic anatomical and physiological similarities. The compact Fugu genome contains the same basic vertebrate blueprint as the human genome in a sequence seven times shorter. This difference is primarily due to the scarcity in Fugu of the large repeat-filled tracts that litter the human genome. The relative compactness of the Fugu genome simplifies the detection and analysis of both gene sequences and gene regulatory elements.

Helobdella robusta Leeches are distinguished from other annelids by anterior and posterior suckers used for locomotion and feeding – on blood or soft body parts of other animals. Helobdella robusta was chosen for whole genome sequencing because of its relatively small genome (~300 Mb) and its use as a model for annelid and lophotrochozoan development.

Homo sapiens, chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes.

Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.

Homo sapiens, chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average.

Nearly one quarter of the genes belong to large tandemly arranged gene families that cover more than 25% of the total chromosome size. The evolutionary landscape is extremely diverse and reveals a chromosome composed of regions of large blocks of 1:1 gene orthology with rodents, scattered regions with more recent gene family expansions/deletions, and segments of both coding and non-coding conservation with the distant fish species Fugu (Takifugu) rubripes.

Laccaria bicolor Comparison of the genomes of the different pathogenic and saprobic fungi with the Laccaria genome will be of interest to a wide range of genome and evolutionary scientists. It will provide critical insights into the genetic makeup of plant-fungus interactions.

Lottia gigantea The gastropod snail Lottia gigantea was chosen as the first lophotrochozoan for whole genome sequencing because the species is an emerging model in evolution and development, ecology, and conservation. The genus is relatively recent in origin and highly diverse, with over 150 species in the Pacific Basin, where they are often conspicuous and important members of the intertidal fauna.

Micromonas pusilla CCMP1545 was isolated from temperate coastal waters near Plymouth, England (North Atlantic/English Channel waters). This is in contrast to the environment from which another strain that is being sequenced (Micromonas RCC299) was isolated. RCC299 was isolated from tropical waters (equatorial Pacific). Micromonas strain CCMP1545 was isolated in 1950 and rendered axenic in 1992.

Micromonas strain RCC299 was isolated in 1998 during a research cruise in the Equatorial Pacific. Subsequently it was rendered clonal and axenic in 2005. RCC299 (also known as NOUM17) was chosen for complete genome sequencing because it was isolated from tropical waters (equatorial Pacific) in contrast to another strain that is being sequenced (CCMP1545) which was isolated from temperate coastal waters, and belongs to a different phylogenetic clade.

Physcomitrella patens ssp patens is a species of moss, which is a basal lineage of land plants, having diverged before the acquisition of well developed vasculature. Thus, it stands in an important phylogenetic position for illuminating the evolutionary development of "higher" plants. Having the full Physcomitrella genome sequence is a great asset for reconstructing the evolution of plant genomes and for informing the community in the functional genomics of plants, just as the mouse, Fugu, Drosophila, and other genomes have informed animal biology.