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

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Etat: Serval
Version: de l'auteur
ID Serval
serval:BIB_5BB2A564D83D
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.
Périodique
Frontiers in Microbiology
Auteur(s)
Bertelli C., Aeby S., Chassot B., Clulow J., Hilfiker O., Rappo S., Ritzmann S., Schumacher P., Terrettaz C., Benaglio P., Falquet L., Farinelli L., Gharib W.H., Goesmann A., Harshman K., Linke B., Miyazaki R., Rivolta C., Robinson-Rechavi M., van der Meer J.R., Greub G.
ISSN
1664-302X (Electronic)
ISSN-L
1664-302X
Statut éditorial
Publié
Date de publication
2015
Peer-reviewed
Oui
Volume
6
Numéro
101
Pages
101
Langue
anglais
Résumé
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.
Pubmed
Web of science
Open Access
Oui
Création de la notice
02/02/2015 19:00
Dernière modification de la notice
08/05/2019 19:06
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