Horizontal gene transfer has been widely known for its important role in eukaryotic evolution. The polyploidization, fragmentation and fusion of genomes may have combined a massive number of genes in a short time, accelerated the evolution of adaptability, and boosted the diversification of species. The genome fusion was realized in the artificial genome shuffling and widely documented cell fusion. The secondary endosymbiosis is a key evolutionary event during the speciation of Stramenopiles; however, it remained unclear whether the process facilitated the adaptation of species to environments. The genome assemblies of a wide taxonomic range of species including brown algae provided us an opportunity to deduce the role played by the secondary endosymbiosis in adapting environments.
The genomes of 42 species including 871,056 genes were grouped with OrthoFinder. The genomes chosen covered those species experienced the secondary endosymbiosis, which included, for example, Stramenopiles, Cryptophyta and Haptophyta, along with the eukaryotic representatives of Archaeplastida, Opisthokonta and Amoebozoa. In addition, we assembled the genomes of Saccharina japonica and Nannochloropsis oceanica from the reads generated by the single molecule real-time sequencing, and incorporated them into the systematic analysis. The eukaryotic tree of life was reconstructed at the whole genome scale instead of a set of genes. In total, 86.7% genes were assigned into 70,370 orthogroups with 36,335 species-specific orthogroups in these 42 species. For the identification of the gene origin, 9,130 orthogroups were found to contain the multiple genes of Stramenopiles, Cryptophyta and Haptophyta, but not only themselves. These genes were sub-grouped into the plant-prone (59-64%), the animal-prone (14-17%), and the non-plant- and non-animal prone (the remained). Such finding indicated that the genome fusion may have occurred during the secondary endosymbiosis, which caused a large-scale horizontal gene transfer, even the domination of the plant-prone genes in some genomes.
The systematic analysis may provide valuable insights into the eukaryotic life tree and deepen our understanding the speciation through the secondary endosymbiosis. The genome assemblies have been avalanching currently, on which a large number of species-specific or Stramenopiles-specific orthogroups can be further explored. The diverse polygenetic distribution of genes within Stramenopiles genomes may also aid to explain the unique tolerance of these species to extreme environments.
 

Genome fusion,Endosymbiosis,Phylogenomics,Stramenopile