Genomes

Plants

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Arabidopsis lyrata
 

Arabidopsis lyrata is the closest well-characterized relative in the same genus as A. thaliana. A. lyrata is an outcrossing diploid and, unlike A. thaliana, has stable and spatially restricted populations or subspecies. Currently, its genome is being sequenced.  Our group will be involved in the annotation of this genome.
 
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Arabidopsis thaliana
 

Arabidopsis thaliana is, since many decades, the model system for many plant biologists, for reasons well known such as its short generation time and its small size. In addition, Arabidopsis has a small genome (about 125Mb). Since the completion of the genome sequence in 2000, biologists and bioinformaticians (including us) have tried hard to identify all the genes on the five chromosomes.  We have also investigated gene and genome duplications in Arabidopsis.
 
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Capsella rubella
 

Also the genome of another close relative of A. thaliana, namely Capsella rubella (the closest genus) is curently being sequenced.  It is estimated that Arabidopsis and Capsella have diverged about 10 million years ago.   Also for this genome, we will be involved in the annotation, as well as in studying the evolution of its genome in comparison with the one of A. thaliana and C. rubella.
 
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Eucalyptus grandis
 

Eucalyptus tree species and hybrids have become the most widely planted hardwoods in the world. Eucalypts are extensively planted in the tropics and subtropics, mostly as exotics. These fast-growing plantations are today supporting multi-billion dollar industries based on eucalypt fibre and hardwood products. The relatively short rotation and extensive use of interspecific hybridization and clonal propagation offers tremendous opportunities for the application of biotechnology in almost all aspects of eucalypt tree improvement. As a result, a major eucalypt genome sequencing project has been initiated in Japan and another being planned in the USA. 
 
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Malus domestica
 

Apples are the fruits of the genus Malus (about 25 species) belonging to the family Rosaceae, the most widely cultivated tree fruit. The apple is one of the pome (fleshy) fruits, in which the ripened ovary and surrounding tissue both become fleshy and edible. The apple flower of most varieties requires cross-pollination for fertilization.
 
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Medicago truncatula
 

Medicago truncatula is the model organism for plant biology in legumes. With 650 genera and over 16,000 species, legumes are second only to grasses in economic importance in world agriculture but progress towards understanding the genetic code of legume crops lags behind other crops such as cereals. The importance of legumes to global agriculture and the need to understand important biological functions not found in existing plant models make M. truncatula exceptionally interesting for sequencing.
 
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Physcomitrella patens
 

The moss Physcomitrella patens is the first Bryophyte genome to be sequenced. Bryophytes, comprising hornworts, mosses and liverworts, occupy an ideal phylogenetic position - halfway between algae and seed plants, for studying the evolutionary history of plants. The moss Physcomitrella patens has emerged as a model plant because of its high homologous recombination frequency that enables efficient gene targeting, and also its relatively simple morphology and its small genome size (~500Mb).
 
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Populus trichocarpa
 

The choice to sequence the poplar genome is not only driven by its great economical value but also because poplar is rapidly becoming the model organism for tree biotechnology. Poplar is a perennial plant and has an estimated genome size of ~520 Mbp divided into 19 chromosomes.  Together with the JGI and Oak Ridge Laboratory, we have  been involved in the  genome annotation of this species.
 
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Solanum lycopersicum
 

The International tomato Genome Sequencing Project aims to sequence the gene-rich euchromatic portions of the twelve tomato chromosomes. An international consortium of sequencing centers is performing most of the genomic sequencing. The tomato genome is comprised of approximately 950 Mb of DNA - more than 75% of which is heterochromatin and largely devoid of genes.
 
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Vitis vinifera
 

Given its cultural and economic importance, wine grape is an obvious candidate for the first woody crop to have its genome deciphered. Of special interest to biologists and breeders are polymorphisms in and around the coding regions. Pinot Noir is highly polymorphic with two clearly distinguishable haplotypes revealing several million SNPs and small indels.
 
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Zostera marina
 

Eelgrass (Zostera) is a genus of plants that are adapted to living in flooded areas, both fresh and salt water. Eelgrasses do not belong to the common grasses (poaceae) but form a separate family: Zosteraceae. They are one of the few vascular plants that can live in salty water. Eelgrass beds are home to a large variety of algae and other plants and they are a major food source for many marine reptiles (eg. turtles). Due to water pollution eelgrasses are becoming an endangered species.
 
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Fungi

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Candida bombicola
 

The yeast Candida bombicola is known to produce sophorolipids and is widely used in industry for the production of surfactans. C. bombicola produces sophorolipid molecules with surfactant properties when grown in a medium composed of two different carbon sources (usually sugar and oil) and a nitrogen source (frequently yeast extract). Sophorolipids are extracellular glycolipids and typically consist of a dimeric sophorose connected by a glycosidic bond to the penultimate hydroxyl group of an 18-carbon fatty acid.
 
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Glomus intraradices
 

Glomus intraradices is an endomychorrhizal fungus. It’s a member of the arbuscular mycorrhiza who stimulate the growth and development of different plant spieces. Worldwide some 150 different species of endomychorrhizal fungi are described, most of which are members of the genus Glomus. These fungi penetrate cells of the root where they form the characteristic tree-like structured (arbuscular) organs for the exchange of sugars and nutrients with the host plant. Most of them also form bulb-like structures in and between root-cells. From the colonized roots outwards mycelia grow into the ground acting as a kind of extension of the root system.
 
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Laccaria bicolor
 

Laccaria bicolor is a basidiomycete that forms ectomycorrhizal associations with different northern forest trees. Because of this it is commonly exploited in forest nurseries to enhance the growth of the seedlings (as a soil inoculant). It is a model organism to study this kind of symbiotic association.  Our team is involved in the genome annotation of Laccaria
 
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Melampsora laricis-populina
 

Confers leaf rust, Melampsora laricis-populina, is the most important and commonly spread leaf-disease among poplars (and confers generally) in Europe. An infected tree has an abnormal high rate of respiration and a weak photosynthesis which forces him to use up his reserves. This results in a reduced growth and badly lignified shoots that then easily freeze and become sensitive to secondary pathogens. Not a single resistant poplar cultivar exists so far, since new virulent strains of Melampsora laricis-populina are developed regularly.
 
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Pichia pastoris
 

Pichia pastoris is a methylotrophic ascomycete fungi which is widely used as a heterlogous protein expression system for basic research and for the production of biopharmaceuticals. It is also an important model organism for investigating peroxisomal proliferation and methanol assimilation. Many properties for example: the high growth rate and high cell density, the tightly controlled methanol-inducible promoters (AOX1 and AOX2) and the efficient heterologous secretion mechanism make P. pastoris as an ideaal expression system.
 
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Animals

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Tetranychus urticae
 

The spidermite (Tetranychus urticae) is a very common garden pest that can cause serious damage to vegetables and other plants. These microscopic spiders are found on the underside of leaves. They extract fluids vital to plants' survival from the leaves, leaving noticeable traces of yellowish white spots, known as stippling, on the top side of the leaves. Another indication are the tiny spider webs on stems and leaves. With the use of a magnifying glass you are able to spot the yellow, white, brown, or red mites and their light colored eggs.

More information can be found at the SpiderMite consortium website
 
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Algae

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Bathycoccus prasinos
 

Bathycoccus is a tiny single-cell coccoid prasinophycean. The prasinophyceae are marine flagellates that form the pico-plankton. Bathycoccus however is one of the few species that seems to lack a flagellate stage in his life-cycle. Bathycoccus has about the same size as a bacterium and is very common in the northern Atlantic Ocean. The cells are covered by delicate overlapping scales, which have a spider 's-web structure and are formed within vesicles (probably Golgi vesicles). The organelles are tightly packed within the cell.
 
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Ectocarpus siliculosus
 

The choice to sequence the genome of Ectocarpus was based on several characteristics including its small size, the fact that the entire life cycle can be completed in Petri dishes in the laboratory, its high fertility and rapid growth (the life cycle can be completed in 2-3 months), the ease with which genetic crosses can be carried out and the relatively small size of the genome. Moreover, the Ectocarpales are closely related to the most economically important brown algal group, the Laminariales. For this organism we are currently performing the genome annotation and subsequent genome wide analyses.
 
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Emiliania huxleyi
 

Emiliania huxleyi, often abbreviated to simply "EHUX", is a species of coccolithophore with a global distribution from the tropics to subarctic waters. It is studied for the extensive blooms it forms in nutrient depleted waters. Like other coccolithophores, E. huxleyi is a single-celled phytoplankton covered with uniquely ornamented calcite disks, coccoliths. Individual coccoliths are abundant in marine sediments and in the case of E. huxleyi, not only the shell, but also the soft part of the organism may be recorded in sediments. Ehux produces a group of chemical compounds that are very resistant to decomposition, known as alkenones.
 
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Micromonas pusilla
 

Micromonas pusilla is one of the smallest known flagellates. M. pusilla is distributed in all seas and often occurs in very large numbers. Under the light microscope it is easily mistaken for a rapidly swimming bacterium. Based on pigment analysis, Micromonas shows affinities with the Mamiellales group of the Prasinophyceae, from which it differs in the lack of scales. It is probably derived from a scale-bearing type like Mantoniella, in which the scales were lost and the flagellum reduced to its present condition, which represents a unique type. Some ultrastructural details are elucidated, but many details remain unknown.
 
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Ostreococcus lucimarinus
 

Three different ecotypes or potential species have been defined for Ostreococcus, based on their adaptation to light intensity. O. lucimarinus is adapted to high light intensities and corresponds to surface-isolated strains. The second (RCC141) has been defined as low-light and includes strains from deeper in the water column. The third (O. tauri) corresponds to strains isolated from a coastal lagoon and can be considered light-polyvalent.
 
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Ostreococcus tauri
 

Ostreococcus tauri is the smallest free-living eukaryote known so far. Its apparent overall simplicity; a naked, non-flagellated cell possessing a single mitochondria and chloroplast, in addition to its small size and ease in culturing, renders it an excellent model organism. We have recently published the genome annotation for this organism, which was the first one for a green alga.
 
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Phaeodactylum tricornutum
 

Phaeodactylum tricornutum belongs to the unicellular brown algal class Bacillariophyceae, or the diatoms. Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are one of the most important constituents of phytoplankton communities in aquatic environments; it is estimated that 20% to 25% of all organic carbon fixation on the planet is carried out by diatoms.
 
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