Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.
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.
Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland.
Claire
C
Bertelli
Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland.
Sébastien
S
Aeby
School of Biology, University of Lausanne Lausanne, Switzerland.
Bérénice
B
Chassot
School of Biology, University of Lausanne Lausanne, Switzerland.
James
J
Clulow
School of Biology, University of Lausanne Lausanne, Switzerland.
Olivier
O
Hilfiker
School of Biology, University of Lausanne Lausanne, Switzerland.
Samuel
S
Rappo
School of Biology, University of Lausanne Lausanne, Switzerland.
Sébastien
S
Ritzmann
School of Biology, University of Lausanne Lausanne, Switzerland.
Paolo
P
Schumacher
School of Biology, University of Lausanne Lausanne, Switzerland.
Céline
C
Terrettaz
Department of Medical Genetics, University of Lausanne Lausanne, Switzerland.
Paola
P
Benaglio
Division of Biochemistry, Department of Biology, University of Fribourg Fribourg, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland.
Laurent
L
Falquet
Fasteris SA Geneva, Switzerland.
Laurent
L
Farinelli
Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland.
Walid H
WH
Gharib
Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany.
Alexander
A
Goesmann
Lausanne Genomic Technologies Facility, Center for Integrative Genomics, University of Lausanne Lausanne, Switzerland.
Keith
K
Harshman
Department of Bioinformatics and Systems Biology, Justus-Liebig-University Giessen Gießen, Germany.
Burkhard
B
Linke
Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland.
Ryo
R
Miyazaki
Department of Medical Genetics, University of Lausanne Lausanne, Switzerland.
Carlo
C
Rivolta
Department of Ecology and Evolution, University of Lausanne Lausanne, Switzerland ; SIB Swiss Institute of Bioinformatics Lausanne, Switzerland.
Marc
M
Robinson-Rechavi
Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland.
Jan Roelof
JR
van der Meer
Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne Lausanne, Switzerland.
Gilbert
G
Greub
annotation; biocuration; chlamydia; genome sequencing; genomics; metabolic pathways; teaching