Genomics, Metagenomics and Phylogenomics of Cyanobacteria

This PhD thesis concerns the genomics, metagenomics and phylogenomics of Cyanobacteria. It is composed of five main parts, of which four are result manuscripts. In the first part (i.e., Introduction), I review a decade of cyanobacterial phylogeny and molecular dating. I show that, in spite of a considerable literature, the global topology of the cyanobacterial tree is incongruent across 9 of the 12 recent studies. I also raise the issue that cyanobacterial datings are all based on ambiguous fossils, since no genomic data are available for unambiguous fossil calibration points. The second part deals with the problem of public genome contamination. I analyzed 440 genomes of Cyanobacteria with a consensus approach of five methods (two based on ribosomal genes and three based on complete genome analysis), and determined that >5% cyanobacterial genomes are contaminated by foreign DNA. The next two parts are metagenomic analyses. The first metagenomic study is a pipeline for properly assembling complete genomes from non-axenic cultures. To this end, I used 17 cyanobacterial cultures from the BCCM/ULC collection of the ULiège and assembled metagenomic reads into 15 genomes with a very low level of contaminants and a high level of completeness. The second metagenomic study deals with the new field of phylometagenomics. Hence, I developed a new syntenic algorithm designed for metagenomes in mind, and applied it to the study of lichenized Cyanobacteria. I found 90 syntenic and collinear genes shared between 28 Nostocales genomes, including 12 new photobiont metagenomes. The subsequent phylogenetic analysis showed a relatively high level of congruence among these genes. Finally, the last part of the thesis is a large constrained SSU rRNA (16S) tree intended to serve as a guide in organism selection for future sequencing projects. It revealed 31 clusters of Cyanobacteria that are completely devoid of representative genomes (<0.1%). Altogether, the results of this PhD work lay the ground for a better phylogenomic study of the Cyanobacteria, taking advantage of new key organisms.

Grantor dc:publisher

ULiège - Université de Liège

Year dc:date

2018

Author dc:creator

• Cornet, Luc

• Life sciences
• Biochemistry, biophysics & molecular biology
• Sciences du vivant
• Biochimie, biophysique & biologie moléculaire

Statement dc:rights

• restricted access
• info:eu-repo/semantics/restrictedAccess

Licence

• http://purl.org/coar/access_right/c_16ec

Language dc:language

en

Identifier

info:hdl:2268/218280

OAI identifier oai:identifier

oai:orbi.ulg.ac.be:2268/218280