ICON LBMGE

Genomes at IGM / LBMGE

		Pyrococcus abyssi GE5 strain "Orsay" sequence has been completed in 1998 by Genoscope (http://www.genoscope.cns.fr/), and deposited in GenBank/Embl under accession number AL096836. Annotation of genomic sequence has been made by Genoscope, Evry France, LBS/IGBMC Illkirch-Graffenstaden France and LBMGE /IGM Orsay France Genome description has been published in: Cohen G., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., Poch O., Prieur D., Quérellou J., Ripp R., Thierry J., Van J. der Oost, Weissenbach J., Zivanovic Y. and Forterre P. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi Mol Microbiol. 2003 47:1495-512. P.abyssi PDF version

		Sulfolobus solfataricus P2 sequence and annotation has been completed in 2001, in a joint effort by IMB/NRC Halifax Canada, MGG/IMB Copenhagen Denmark, Wageningen University, Laboratory of Microbiology, The Netherlands and LBMGE /IGM Orsay France. Accession number in GenBank is AE006641 . Genome description has been published in: Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 14, 7835-7840, July 3,2001. Sulfolobus solfataricus P2 PDF version

	Bacteriophage T5 st0 deletion mutant + wt insertion	Bacteriophage T5 Sequence subcontracted to Integrated genomics This a joint project by: Transports Membranaires de Macromolécules, IBBMC Orsay France LBMGE IGM, Orsay France EAN IGM, Orsay France labs Unpublished GenBank accession numbers: AY692264 (st0 deletion mutant) & AY734508 wild type insertion

	Kluyveromyces lactis (image from wikimedia.org)	Kluyveromyces lactis Sequence completed by Genoscope (http://www.genoscope.cns.fr/) Annotation of K. lactis is a joint project by IGM / Genolevures / Institut Pasteur Published in : Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic Y, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL. Genome evolution in yeasts. Nature. 2004 Jul 1;430(6995):35-44. Zivanovic Y, Wincker P, Vacherie B, Bolotin-Fukuhara M, Fukuhara H. Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis. FEMS Yeast Res. 2005 Feb;5(4-5):315-22.

	Thermococcus gammatolerans	Thermococcus gammatolerans Free access Shotgun sequence by Genoscope This a project by: Laboratoire de Genomique des Archaea, IGM Orsay France Publication in Genome Biology on 06/11/09: Genome analysis and genome-scale proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Y. Zivanovic, J. Armengaud, A. Lagorce, C. Leplat, P Guerin, M. Dutertre, V. Anthouard, P. Forterre, P. Winker, and F. Confalonieri GenBank accession number: CP001398
	ΦX174	Viral Genomes : Microviridae in Sphagnum- dominated peatlands Free access Isolation / sequencing by UMR CNRS 6553 -ECOBIO, Universite de Rennes 1, Rennes, France Functional and Environmental Genomics platform (OSUR), Rennes, France This a project by: INSU-CNRS EC2CO program (VIRTOU) and grants from the University of Rennes/CNRS and from the observatoire des Sciences de l'Univers Rennes(OSUR) Publication in Frontiers in Microbiology: Diversity and comparative genomics of Microviridae in Sphagnum-dominated peatlands. Quaiser A, Dufresne A, Ballaud F, Roux S, Zivanovic Y, Colombet J, Sime-Ngando T and Francez A-J (2015) Front. Microbiol. 6:375. \| http://dx.doi.org/10.3389/fmicb.2015.00375 GenBank accession numbers: KM589498-KM589516
	Cruciviridae	Viral Genomes : Cruciviruses: chimeric viruses in Sphagnum- dominated peatlands Free access Isolation / sequencing by UMR CNRS 6553 -ECOBIO, Universite de Rennes 1, Rennes, France Functional and Environmental Genomics platform (OSUR), Rennes, France This a project by: INSU-CNRS EC2CO program (VIRTOU) and grants from the University of Rennes/CNRS and from the observatoire des Sciences de l'Univers Rennes(OSUR) Publication Quaiser, A., Krupovic, M., Dufresne, A., Francez, A. J., & Roux, S. (2016). Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands. Virus evolution, 2(2), vew025. \| https://doi.org/10.1093/ve/vew025 GenBank accession numbers: KX388494-- KX388530 / MetaVir Project id: 8195
	Vampirococcus lugosii	Vampirococcus lugosii Free access Isolation / amplification / sequencing by Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France. Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, Orsay, France This a project by: ESE, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France. I2BC, CNRS, Université Paris-Saclay, Orsay, France Publication NATURE COMMUNICATIONS \| (2021)12:2454 \| https://doi.org/10.1038/s41467-021-22762-4 Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii . David Moreira, Yvan Zivanovic, Ana I. López-Archilla, Miguel Iniesto & Purificación López-García GenBank accession number: PRJNA678638
	Deinococcus radiodurans R1 ATCC 13939	Deinococcus radiodurans R1 ATCC 13939 Free access Isolation / amplification / sequencing by Universite Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France. Publication Cells \| (2021) Sep 25;10(10):2536. \| https://doi.org/10.3390/cells10102536 Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses. . Eugenie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri F. GenBank accession numbers: CP068791, CP068792, CP068793, CP068794
	Candida glabrata CBS138	Nakaseomyces genomes backup database Free access Maintained at Universite Paris-Saclay, CEA, CNRS, Institut Diversité, Écologie et Évolution du Vivant (IDEEV), 91198 Gif-sur-Yvette, France. This is a custom database of publicly available Nakaseomyces genomes/scaffolds for the benefit of local users. Publications (...) GenBank accession numbers:

Pyrococcus abyssi is an hyperthermophilic euryarcheaon thriving in deep-sea hydrothermal vents , growing optimally at 96°C in strict anaerobic conditions and metabolizing sulfur. It has been sampled in the North Fiji basin (SW Pacific) at 2000 mt depth in 1989.
Sulfolobus solfatricus is an aerobic crenarchaeon that grows optimally at 80°C and pH 2-4 metabolizing sulfur which growths in volcanic solfataras. It is the most widely studied organism of the crenarchaeal branch of the Archaea
Bacteriophage T5 is a lytic, linear, double stranded "nicked" DNA phage belonging to Siphoviridae family. The phagic infection is a two step mechanism, in which the first-step transfer segment allows expression of pre-early genes necessary for complete DNA transfer and initiation of the lytic cycle. We have sequenced the deletion mutant st0, a widely used laboratory strain for primary sequence determination. Subsequently, full wild type genome has been reconstructed by incorporating the sequence of the wild type insertion from HER28 strain (obtained from Reference Center For Bacterial Viruses, Laval University, Quebec, Canada)
Kluyveromyces lactis, a yeast commonly used in genetic studies, cheese and yogurt production, and could potentially be used to produce drug compounds.
A large scale comparative genomic study as been undertaken, leading to sequencing and comparison of 3 other hemiascomycetous yeasts (Candida glabrata, Debaryomyces hansenii, and Yarrowia lipolytica.)
Thermococcus gammatolerans, was isolated from samples collected from hydrothermal chimnneys. This organism withstands 5 kGy irradiation without any detectable lethality and thus it is one of the most radioresistant organisms known amongst the Archaea. Complete sequencing, assembly and annotation was performed at LGA, Orsay. Complete proteome analysis performed in collaboration with CEA, DSV, IBEB Laboratoire de Biochimie des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France. Transcriptonal response to Cadmium and gamma-irradiation analysis performed at LGA.

LBMGE has been directly involved in genome sequencing of these two hyperthermophilic archeons during the past years.
Both strains are widely studied model microorganisms in various fields of investigation such as studies on adaptation to extreme temperatures and pH growth conditions, aerobic and anaerobic sulfur metabolism analysis, molecular deciphering of DNA replication mecanism in archaea, phylogeny and rooting of the tree of life, comparative genomics of closely related strains and many others.

This page provides direct links to genomic annotation databases for P. abyssi and S. solfataricus, bacteriophage T5 and T gammatolerans
All databases on this site are maintained by Y. Zivanovic.

Some references related to these projects:

P. abyssi:

Lopez, P., Philippe, H, Myllykallio, H. and Forterre, P.
Identification Of Putative Chromosomal Origins Of Replication In Archaea.
Mol. Microbiol. 32, 883-886 (1999)
H. Myllykallio, P. Lopez, P. López-García, R. Heilig, W. Saurin, Y. Zivanovic, H. Philippe, and P. Forterre
Bacterial Mode Of Replication With An Eukaryotic-Like Machinery In A Hyperthermophilic Archaeon
Science, 288, 2212-2215 (2000)
O. Matte-Tailliez, Y. Zivanovic and P. Forterre
Mining archaeal proteomes for eukaryotic proteins with novel functions: the PACE case
Trends Genet. 16, 533,536 (2000) link on this site : PACE Proteins
Zivanovic, Y., Myllykallio, H. and Forterre, P.
Bacterial genomic reorganization upon DNA replication.
Science 292, 803a (2001)
Zivanovic Y., Lopez P, Philippe P and Forterre P
Pyrococcus genome comparison evidences chromosome shuffling-driven evolution.
Nucleic Acids Research, 30, 2656-62 (2002)
Cohen G., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O., Poch O., Prieur D., QuŽrellou J., Ripp R., Thierry J., Van J. der Oost, Weissenbach J., Zivanovic Y. and Forterre P.
An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi
Mol. Microbiol. in Press (2002)

S. solfataricus:

She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Gordon, P., Allard, G., Awayez, M.J., Chan-Weiher, C-Y., Clausen, I.G., Curtis, B., De Moors, A., Erauso, G., Gordon, P.M.K., Heikamp de Jong, I., Jeffries, A., Kozera, C.J., Medina, N., Peng, X., Phan, H., Redder, P., Schenk, M.E., Theriault, C., Tolstrup, N., Charlebois, R.L.M., Doolittle, W.F., Duguet, M., Gaasterland, T., Garrett, R.A., Ragan, M., Sensen, C.W. and Van der Oost, J.
The genome sequence of the crenarchaeon Sulfolobus solfataricus P2.
Proc. Natl. Acad. Sci. USA 98, 7835-7840. (2001)
Forterre, P., Confalonieri, F. and Knapp, S.
Identification Of The Gene Encoding Archaeal-Specific Dna Binding Proteins Of The Sac10b Family
Mol. Microbiol. 32, 669-670 (1999)
R. Charlebois, R. Singh, C.C.-Y. Chan-Weilher, G. Allard, C. Chow, F.,Confalonieri, B. Curtis, M. Duguet, D. Faguy, T. Gaasterland, R. Garrett, A.,Jeffries, C. Kozera, N. Kushwala, E. Lafleur, N. Medina, X. Peng, S.,Penny,Q. She,A. Stjohn, J. Van Der Oost, F. Young, Y. Zivanovic, W.,Doolittle, M. Ragan & C. Sensen.
Gene Content and Organization Of A 281 Kbp Contig From The Genome Of The Extremely Thermophilic Archaeon Sulfolobus Solfataricus P2.
Genome 43, 116-36 (1999)
Q She, F Confalonieri, Y Zivanovic, N Medina, A Billault, M J. Awayez, H P, Thi-Hgoc, B-T T Pham, J Van Der Oost, M Duguet, and R Garrett
A Bac Library and Paired-PCR Approach To Mapping and Completing The Genome Sequence Of Sulfolobus Solfataricus P2: An EC Perspective
DNA Seq., 11(3-4),183-92. (2000)
Brügger K., Redder P., She Q., Confalonieri F., Zivanovic Y. and Garrett R. A.
Mobile elements in archaeal genomes
FEMS Microb. Lett., 206, 131-141 (2002)

Kluyveromyces lactis:

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic Y, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL.
Genome evolution in yeasts.
Nature. 2004 Jul 1;430(6995):35-44.
Zivanovic Y, Wincker P, Vacherie B, Bolotin-Fukuhara M, Fukuhara H.
Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis.
FEMS Yeast Res. 2005 Feb;5(4-5):315-22.

Thermococcus gammatolerans:

Recovery of ionizing-radiation damage after high doses of gamma ray in the hyperthermophilic archaeon Thermococcus gammatolerans.
Tapias A, Leplat C, Confalonieri F.
Extremophiles. 2009
Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to Cadmium
A Lagorce, A Fourcans, M Dutertre, B Bouissiere, P Forterre, X Gidrol, Y Zivanovic And F Confalonieri
PLoS One. 2012;7(7):e41935. doi: 10.1371/journal.pone.0041935. Epub 2012 Jul 27. PMID: 22848664; PMCID: PMC3407056.
Genome analysis and genome-scale proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
Y. Zivanovic, J. Armengaud, A. Lagorce, C. Leplat, P Guerin, M. Dutertre, V. Anthouard, P. Forterre, P. Winker, and F. Confalonieri
Genome Biol. 2009;10(6):R70. doi: 10.1186/gb-2009-10-6-r70. Epub 2009 Jun 26. PMID: 19558674; PMCID: PMC2718504.