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Recombination and horizontal gene transfer through the lens of phylogenomics

Research output: Book/anthology/dissertation/reportPh.D. thesisResearch

With ever-increasing numbers of genome sequences, bioinformaticians are in a
privileged position to propose novel biological questions. In this dissertation, I
investigated how modes of recombination—homologous recombination and horizontal
gene transfer (HGT)—impact the genetic variation and subsequent evolution
of the tree of life.
I first evaluate the rate and the mode of HGT among 196 bacterial genome
sequences of five closely-related species of the genus Rhizobium (Rhizobium leguminosarum:
gsA, gsB, gsC, gsD, and gsE). This study shows that HGT was
generally very restricted, with most genes following the species-tree phylogeny.
Exceptions were genes located on symbiosis plasmids and two chromosomal islands;
conjugation was the likely mode of these transfers. These results contradict the
longstanding notion that high rates of HGT would blur bacterial species delineation.
Whether homologous recombination has a net beneficial or detrimental effect on
adaptive evolution () has remained largely unexplored in bacteria. By evaluating
polymorphism data across our Rhizobium species dataset, we observed substantial
amounts of within-species homologous recombination. We also find a positive
correlation between recombination and both in the intra and interspecies levels.
These results suggest that homologous recombination, as an adaptive evolutionary
force, has been employed long before eukaryotes.
In sexually reproducing organisms, meiotic recombination is initiated by the
deliberate infliction of numerous double-strand breaks (DSBs) in the genome, the
repair of which yields crossover and non-crossover resolutions. In most mammals,
these DSBs are specified through the binding of PRDM9 and the deposition of
H3K4me3 and H3K36me3 marks. Despite its evolutionary importance, PRDM9 has
been lost numerous times across vertebrates evolution. To further our understanding
of PRDM9 evolution and investigate its coevolution with other genes, we first
generated and analyzed expression data from testis tissues of two different reptiles
(Anolis carolinensis, Sceloporus undulatus) and fish (Astyanax mexicanus and Clupea
harengus). These data suggest an ancient loss of PRDM9 in squamates and a partial
PRDM9 loss in both fish species. We then examined the coevolution of PRDM9
with meiosis-related genes. We confirmed previous reports that ZCWPW1 is tightly
co-evolving with PRDM9, consistent with its newly discovered role in reading
the epigenetic modifications made by PRDM9 and enabling DSB repair. We
further found a second gene, ZCWPW2, which has both domains needed to read
marks laid down by PRDM9. Its phylogenetic distribution makes it a plausible
candidate for the link between PRDM9 binding and the recruitment of SPO11
and other associated proteins.
Through the lens of phylogenomics, I explored the impact of recombination
and HGT on the evolution of prokaryotes and eukaryotes.
Original languageEnglish
Place of publicationAarhus
PublisherAarhus Universitet
Number of pages180
Publication statusPublished - Aug 2020

    Research areas

  • rhizobium, Phylogenomics, Recombination, Genetic, PRDM9, Evolution

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ID: 195932962