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

Frontiers in Microbiology
Claire BertelliGilbert Greub

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 9...Continue Reading

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Citations

Aug 25, 2015·Microbes and Infection·Marie de BarsyGilbert Greub
Oct 7, 2015·Bacteriophage·Louise Temple, Lynn Lewis
May 20, 2015·Pathogens and Disease·Carole Kebbi-BeghdadiGilbert Greub
Apr 11, 2015·Pathogens and Disease·Brigida RusconiGilbert Greub
Aug 16, 2016·Genome Biology and Evolution·Claire BertelliGilbert Greub
Nov 7, 2020·Current Biology : CB·Stephan KöstlbacherMatthias Horn
Mar 7, 2020·Current Biology : CB·Jennah E DharamshiThijs J G Ettema
Jul 1, 2021·Nature Communications·Stephan KöstlbacherMatthias Horn

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Methods Mentioned

BETA
RNA-seq
ChIP-seq
electron microscopy
PCR

Software Mentioned

Consed
Linux
BLASTN
GenDB
HMM
R
SOAPdenovo
GEBA
TIGRfam
Mauve

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