Site du Genoscope

Sequencing

2007-06-06T08:07:47Z

Projects

2007-06-06T13:40:55Z

Click on one of the 4 divisions (Microorganisms, Plants, Fungi or Animals).
For targeted research, type the name of the organism in the search engine.

the Mediterranean basin accounts for 20% of the world production of citrus fruit

2007-06-28T14:56:38Z

From an economic point of view, citrus fruits occupy first place in terms of world fruit production, with 95 million tons produced annually. The Mediterranean basin accounts for 20% of the total by itself, with one major producer: Spain.

Because of their content of micronutrients (vitamin C, carotenoids, polyphenols, etc.), citrus fruits contribute to nutritional balance for both Northern and Southern populations. Nutritional and organoleptic qualities are thus important components of selection projects at the international level. This production network is confronted with increasing biotic and abiotic pressures, and global climate change has augmented the risk of extension of emerging diseases from hot regions to the Mediterranean Basin.

Within the framework of the development of integrated protection systems, the creation of varieties and graft suports which combine tolerance to these constraints and good quality characteristics constitutes a major challenge. Because of the length of the juvenile phase (5 to 10 years) and the large number of offspring to be analyzed, a knowledge of the physiological and genetic determinants of selected characteristics and the development of early selection markers are essential.
Compared to their economic importance, the international research plans are insufficient, and the establishment of close collaborations between groups seems necessary. The creation of an international consortium on sequencing and genomics of citrus fruit, which is currently underway, seems to be a step in the right direction. This project fits into studies on integrative biology being performed in the domains of the response to abiotic stress, quality development and developmental biology by French and Spanish pluridisciplinary groups engaged in projects for the creation of new varieties and graft supports. It should contribute to the development of a European pole for research on citrus fruit cultivation, and to a good positioning of French groups within the international consortium on citrus fruit genomics.

cDNA library

2007-06-28T15:00:12Z

Genoscope is undertaking the sequencing from 5' of a collection of about 35,000 full-length cDNAs from Nules Clementines (Citrus clementina), with a sequencing volume of 35,000 reads.

Contacts:
Patrick Wincker (Genoscope) - Raphaël Morillon (INRA)

A bacterial pathogen responsible for nosocomial infections

2007-07-04T14:14:15Z

The Acinetobacter genus belongs to the gamma subdivision of Proteobacteria, and to the Moraxellaceae family. Genoscope has already sequenced the genome of Acinetobacter sp. ADP1, a soil isolate. A. baumannii, on the contrary, is a pathogenic species. In the industrialized countries of the Northern Hemisphere, it causes nosocomial infections only. Its presence in this type of infection can be explained by its very high capacity to acquire antibiotic resistance. The situation is different in tropical countries, where A. baumannii is found in community-acquired infections (contracted outside of hospital). These infections are essentially pneumonias associated with bacteremia (presence of bacteria in blood) and are found in alcoholic patients.

We are sequencing the genome of two A. baumannii strains. The first one, named VEB, is representative of nosocomial strains. It is responsible for a hospital epidemic, associated with high mortality, that broke out in the north of France. The VEB strain is antibiotic multiresistant. The second strain, named SDF, is responsible for community-acquired infections. It belongs to a group of new A. baumannii

strains which have been found to have high sensitivity to antibiotics. These strains were isolated from the interior of body lice collected on homeless people living in France. Given that the louse interior is usually sterile, the presence of these strains can only be due to cryptic bacteremic episodes.

It will be interesting to compare the genomes of a nosocomial, multiresistant strain and a community-acquired, multisensitive strain, in order to identify the factors responsible for their adaptation to very different environments and their different pathogenic potential.

Whole genome shotgun

2007-07-04T14:18:13Z

Two strains of Acinetobacter baumannii are being sequenced in Genoscope : a nosocomial strain which is antibiotic multiresistant (VEB) and a community, multisensitive strain (SDF).

The genome size for each strain is estimated at 4 Mb. Sequence coverage for each genome is 12X. Three libraries are being sequenced : 30,000 clones with 3 kb inserts in a pNAV vector (high copy number shuttle vector between E. coli and Acinetobacter), 11,500 clones with 10 kb inserts in a pCNS vector (low copy number) and nearly 4,000 clones with 20-25 kb inserts in a miniBAC vector (pBBC).

A manual finishing stage will be performed at Genoscope.

Contacts:
Valérie Barbe (Genoscope) - Didier Raoult, Catherine Robert (UMR 6020)

A thermotolerant polychete annelid

2007-07-04T14:30:01Z

The Annelids are characterized by the appearance of a coelomic cavity and segmentation. These morphologic innovations are due to the appearance of major genetic programs of differentiation and development in the Metazoans during the course of evolution. At this time, Annelids are largely under-represented in sequence databases (less than 1000 protein sequences. The construction and sequencing of a complete cDNA library from Alvinella pompejana will lead to the rapid generation of molecular information about this phylum. This project will be complementary to the French project for the sequencing of the genome of the Annelid, Platynereis dumerillii. In fact, the cDNA sequences of Alvinella will be very useful in the annotation of the genome of Platynereis dumerilii, and the sequences of the two organisms will open the door to numerous comparisons.

In addition to its evolutionary interest, A. pompejana exhibits a thermotolerance which is exceptional in a eukaryote (from 20 to more than 80 degrees), which makes this an ideal model organism for the production of thermostable proteins of animal origin for the following applications :

the determination of the structure of eukaryotic proteins, the reconstitution and crystallization of molecular complexes and for proteomic studies in the broad sense

the study of complex biologic systems (molecular adaptation to thermic, oxydative and chemical stress, etc.)

medical and biotechnological applications (study of homologs of proteins responsible for human diseases, acquisition of antibacterial peptides, production of thermostable industrial enzymes, blood substitutes, etc.)

cDNA library

2007-07-04T14:33:49Z

Within the framework of this project, three cDNA libraries will be produced at Genoscope :

a library from the whole animal,
a second one from the gills
and a third from the ventral tissue of the animal, which has the property of being free of bacteria.

The cDNAs obtained from RNAs by the “oligo-capping” method will be cloned in the plasmid vector pMe18S-f13.

About 50,000 clones from each library will be sequenced at the 5' end, and then the clones which contain complete ORFs will be rearranged and sequenced from the 3' end.

Contacts:
Patrick Wincker (Genoscope) - Olivier Poch (IGBMC)

A cyanobacterium of many interests

2007-07-04T14:39:54Z

The genus Arthrospira Stizenberger includes filamentous Oscillatoriaceae with multicellular cylindrical trichomes arranged in an helicoidal shape, with cross-walls visible by light microscopy, and containing gas-vesicles. The trichomes are motile and their diameters vary generally from 5 to 12 µm. Cells are generally shorter than broad or isodiametric (Castenholz et al., 2001).

Many strains are industrially cultivated as a health food due to their richness in proteins, essential fatty acids (linoleic and gamma-linoleic acid), vitamins (provitamin A, vitamin B12, ...) and minerals (iron source), and are currently commercialised under the name “Spirulina”. The confusion between both names has arisen due to Geitler's decision to unite the two genera Arthrospira Stizenberger and Spirulina Turpin in his Flora in 1932, on the basis of their coiled trichomes (Geitler, 1932). However, the true Spirulina are not related to Arthrospira (Nelissen et al., 1994).

Organisms of the Arthrospira genus are commonly found in marine, brackish water and saline lake environments of tropical and semi-tropical regions (Castenholz et al., 2001). The precise origin of Arthrospira sp. PCC 8005 is unknown. It belonged to a set of 4 strains from India, Kenya, Mexico and Peru deposited in the Pasteur Collection of Cyanobacteria (PCC) by Dr. Jeeji-Bai in 1980, but the notebook with the information was lost by a student (R. Rippka, personal communication). However, its ITS sequence is identical to the one of another indian strain (A. indica MCRC straight) given later by Dr. Jeeji-Bai to Scheldeman et al. (1999).

Arthrospira was consumed by the Aztecs in the sixteenth century, and is presently still a source of proteins for the Kanembu tribe in Chad. It is harvested in small wadi by women, dried, and sold as “ dihé ” at the market place.

It is well known that cyanobacteria have played a major role in the evolution of life on Earth. In particular, they are thought to be the main cause of the oxygenation of our atmosphere. Nowadays, they still make a significant contribution to the global oxygen production in the oceans (Garcia-Pichel, 2000). They even became locally dominant primary producers of oxygen, carbon and organics in extreme environments such as hot and cold deserts, hot springs and hypersaline environments (Garcia-Pichel, 2000). Because of these particular characteristics, Arthrospira was selected as a complementary food source and for the production of oxygen in the Life-Support system MELiSSA (Micro-Ecological Life Support System) that is constructed for long-term spatial missions.

References:

CASTENHOLZ, RW, RIPPKA, R, HERDMAN, M & WILMOTTE, A. (2001) Form-genus I. Arthrospira Stizenberger 1852. In: Bergey's Manual of Systematic Bacteriology, Vol. 1 (D. R. Boone & R.W. Castenholz, eds.). Springer, NewYork, USA , pp 542-543.
GARCIA-PICHEL, F. (2000). Cyanobacteria. In: Encyclopedia of Microbiology, Vol. 1. A. Press, pp 907-929.
GEITLER, L.(1932) Cyanophyceae. In: Rabenhorst's Kryptogamenflora von Deutschland, Österreich und der Schweiz, Leipzig, Akad. Verslagsges. 1932. Reprinted 1971, New York, Johnson, pp. 1-1196.
NELISSEN, B., WILMOTTE, A., NEEFS, J.M. & DE WACHTER, R. (1994) Phylogenetic relationships among filamentous helical cyanobacteria investigated on the basis of 16S ribosomal RNA gene sequence analysis. In: Systematic and Applied Microbiology, vol 17, pp 206-210.
SCHELDEMAN, P., BAURAIN, D., BOUHY, R., SCOTT, M., MUHLING, M., WHITTON, B.A., BELAY, A.& WILMOTTE, A. (1999) Arthrospira (“Spirulina”) strains from four continents are resolved into only two clusters, based on amplified ribosomal DNA restriction analysis of the internally transcribed spacer. In: FEMS Microbiology Letters 172: 213-222.

Whole genome shotgun

2007-07-04T14:43:35Z

Genoscope is undertaking the sequencing of the cyanobacterium, Arthrospira sp. PCC8005.

The size of the genome of this bacterium is estimated at about 5,7 Mb. The genome will be sequenced at 12X depth, using three libraries: about 33,000 inserts of 3 kb cloned in a pcdna2.1 vector (high copy number), about 11,000 inserts of 10 kb cloned into a pCNS vector (small copy number) and close to 6,000 inserts of 40 kb cloned in a fosmid vector (pCC1Fos).

Contacts:
Valérie Barbe (Genoscope)
Max Mergeay (SK/CEN) - Larissa Hendrickx (SK/CEN)