Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina–Blastocystis Stramenopile Lineage

Abstract

Lateral gene transfer is a very common process in bacterial and archaeal evolution, playing an important role in the adaptation to new environments. In eukaryotes, its role and frequency remain highly debated, although recent research supports that gene transfer from bacteria to diverse eukaryotes may be much more common than previously appreciated. However, most of this research focused on animals and the true phylogenetic and functional impact of bacterial genes in less-studied microbial eukaryotic groups remains largely unknown. Here, we have analyzed transcriptome data from the deep-branching stramenopile Opalinidae, common members of frog gut microbiomes, and distantly related to the well-known genus Blastocystis. Phylogenetic analyses suggest the early acquisition of several bacterial genes in a common ancestor of both lineages. Those lateral gene transfers most likely facilitated the adaptation of the free-living ancestor of the Opalinidae–Blastocystis symbiotic group to new niches in the oxygen-depleted animal gut environment.

Improved Reference Genome forCyclotella crypticaCCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

“…Contaminant scaffolds can be identified using the Blobtools pipeline on the basis of GC content, sequencing coverage, and taxonomic assignment via BLAST searches to reference protein databases. This pipeline has been used to identify and remove contaminants from other microbial eukaryotic genome projects (Koutsovoulos et al 2016;Nowell et al 2018;Yubuki et al 2020). During the construction of the version 2.0 assembly, we used the Blobtools pipeline to identify and remove all scaffolds from the metagenome assembly with lengths less than 1 kb or with a taxonomic assignment to bacteria, archaea, or viruses ( Figure S2).…”

The Genome of the Mitochondrion-Related Organelle in Cepedea longa, a Large Endosymbiotic Opalinid Inhabiting the Recta of Frogs

“…The stramenopiles comprise photosynthetic and nonphotosynthetic lineages. All species in Opalinata live as parasites or commensals in the intestinal tracts of amphibians, lizards, birds and mammals [ 20 , 27 , 34 ]. Although the ultrastructure of the C. longa MRO is similar to the standard aerobic mitochondria (double-membrane structure and cristae formed by the inner membrane), it lacks genes encoding the complex III-IV of the electron transport chain (ETC) and ATP synthase; this may be because C. longa mainly inhabits the recta with low oxygen concentration [ 26 ].…”

“…The ancestor of Opalinidae and Blastocystis was most probably free-living since their closest relatives are all free-living [ 27 , 33 ]. In addition, Blastocystis is better adapted to anaerobic conditions than Opalinidae [ 34 ]. On this basis, opalinids may represent an intermediate adaptation stage between the conventional aerobic mitochondria and derived anaerobic MROs [ 34 ].…”

“…In addition, Blastocystis is better adapted to anaerobic conditions than Opalinidae [ 34 ]. On this basis, opalinids may represent an intermediate adaptation stage between the conventional aerobic mitochondria and derived anaerobic MROs [ 34 ].…”

Contamination detection in genomic data: more is not enough

“…HGT is not limited to bacteria and can involve eukaryotes too. For example, numerous cases of gene exchange between bacteria and fungi have been reported [ 70 – 75 ]. Two different problems can be distinguished when considering HGT and contaminations.…”