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.