Prok2EukLateralGeneTransfer

Lateral gene transfer (also known as Horizontal Gene Transfer) is the
transmission of genetic material between phylogenetically unrelated
organisms. Previous studies have been showing the importance of this
process for the evolution of unicellular eukaryotes, particularly those
living in highly competitive niches such as the herbivore gut.
Pyromices sp. is an obligate anaerobic chytrid fungus that grows as a
commensal organism in the gut of mammalian herbivores, possessing
hydrogenosomes instead of mitochondria, producing hydrogen, and playing a
key role in the digestion of plant cell wall material. These particular
features make its genome particularly valuable for the study of the
evolution and adaptation of unicellular eukaryotes to the cellulose-rich
and anaerobic environment of the herbivore gut.
Here we performed a detailed large-scale lateral gene transfer (LGT)
analysis of the genome from the chytrid fungus Piromyces sp. strain E2.
For this we set out to elucidate (i) which proteins were likely
transferred to its genome, (ii) from which bacterial donor species, and
(iii) which functions were laterally acquired.
Using sequence comparison and phylogenetic analyses, we have found 704
LGT candidates, representing nearly 5% of the Piromyces sp. orfeome
(i.e. the complete set of open reading frames), mostly transferred from
Firmicutes, Fibrobacteres, Bacteroidetes and Proteobacteria, closely
following the microbial abundance reported for the herbivore gut. With
respect to the functional analysis, the LGT candidate set includes
proteins from 250 different orthologous groups, with a clear
over-representation of genes belonging to the Carbohydrate Transport and
Metabolism functional class. Finally, we performed a graph density
analysis on the metabolic pathways formed by the LGT candidate proteins,
showing that the acquired functions fit cohesively within Piromyces
metabolic network, and are not randomly distributed within the global
KEGG metabolic map.
Overall, our study suggests that Piromyces' adaptation to living
anaerobically and in the a cellulose-rich environment has been
undoubtedly fostered by the acquisition of foreign genes from bacterial
neighbors, showing the global importance of such evolutionary mechanisms
for successful eukaryotic thriving in such competitive environments.
This work represents the Datasets generated to study the contribution of
Lateral Gene Transfer to the evolution of eukaryotic unicellular
organisms, reported in the manuscript:"Contribution of Lateral Gene Transfer to the evolution of the eukaryotic fungus Piromyces sp. strain E2: Massive Lateral Gene Transfer of genes involved in carbohydrate metabolism."
-Supplementary data 1. LGT candidate set: List of candidate Piromyces LGT proteins that are predicted to be hydrogenosomal (suppData-hydrogenosomePred.xlsx).

-Supplementary data 2. LGT candidate set: Mapping the LGT candidates to orthologous groups (functional classification) (suppData-OGs.txt).
-Supplementary data 3. LGT assessment: All phylogenies computed (in Newick format) used to find the LGT candidates (suppData-trees.tar.gz).
-Supplementary figure 1. Distributions of the observed and random graph densities calculated (suppFigure-densityDist.pdf).