Phylogenomic investigation of lateral gene transfers among grasses

Lateral gene transfer (LGT) transcends the species barriers and allows the acquisition of genetic material that adds novelty to the recipient species. This process is widely reported in prokaryotes, but its existence in eukaryotes remained controversial until recently. The extent and adaptive significance of eukaryotic LGT remains poorly explored. In this thesis, I assess the extent of LGT among grasses and whether some groups or genes are more prone to such interspecific exchanges. I first scan for LGT in the genomes of 17 grass species covering the breadth of the family, and identify LGT in 13 of them, including wild and crop species. The rate of LGT appears higher in rhizotomous species and between closely-related groups. I then examine in further details grass genes and species in which LGT had been previously documented to evaluate the factors that promote LGT. I reconstruct the evolutionary history of an important enzyme of the C4 pathway, and show that it has been laterally transferred at least six times in distantly-related groups of C4 grasses. Its importance for the C4 pathway and the requirement for gene duplications before co-option likely made LGT of this gene especially beneficial. Finally, I compare the genomes of two grass species, one of which was known to have received genes from the other, to test the hypothesis that LGT happens bidirectionally. While my analyses detected multiple LGT from the known donor, very few candidates seem to have travelled in the other direction, suggesting that LGT can be unidirectional. Overall, my work revealed that LGT is rampant among grasses, but that some genes and species are more often involved in such transfers than expected by chance. These investigations should be expanded when numerous grass genomes are available to precisely quantify the rates of LGT among lineages and across the genomes.