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Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

Bertelli, Claire and Aeby, Sébastien and Chassot, Bérénice and Clulow, James and Hilfiker, Olivier and Rappo, Samuel and Ritzmann, Sébastien and Schumacher, Paolo and Terrettaz, Céline and Benaglio, Paola and Falquet, Laurent and Farinelli, Laurent and Gharib, Walid H. and Goesmann, Alexander and Harshman, Keith and Linke, Burkhard and Miyazaki, Ryo and Rivolta, Carlo and Robinson-Rechavi, Marc and van der Meer, Jan Roelof and Greub, Gilbert. (2015) Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Frontiers in Microbiology, 6. p. 101.

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Abstract

With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.
Faculties and Departments:03 Faculty of Medicine
09 Associated Institutions > Institute of Molecular and Clinical Ophthalmology Basel (IOB)
UniBasel Contributors:Rivolta, Carlo
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Frontiers Media
e-ISSN:1664-302X
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:05 Mar 2021 10:40
Deposited On:05 Mar 2021 10:40

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