Horizontal functional gene transfer from bacteria to fishes

Abstract

Invertebrates can acquire functional genes via horizontal gene transfer (HGT) from bacteria but fishes are not known to do so. We provide the first reliable evidence of one HGT event from marine bacteria to fishes. The HGT appears to have occurred after emergence of the teleosts. The transferred gene is expressed and regulated developmentally. Its successful integration and expression may change the genetic and metabolic repertoire of fishes. In addition, this gene contains conserved domains and similar tertiary structures in fishes and their putative donor bacteria. Thus, it may function similarly in both groups. Evolutionary analyses indicate that it evolved under purifying selection, further indicating its conserved function. We document the first likely case of HGT of functional gene from prokaryote to fishes. This discovery certifies that HGT can influence vertebrate evolution.

Figure 1. Species-tree for representative eukaryotes and the distributions of XP_001335286.1 homologs among the taxa.

Representative eukaryotic clades were selected from among many to simplify depiction of the distributions of the homologs. Bacteria was used as the outgroup. Genes that were most evenly sampled across major clades were used to construct the phylogeny with ML methods. Red triangles indicate species that possess XP_001335286.1 homologs.

Figure 2. Phylogenetic trees of XP_001335286.1 homologs.

The Bayesian unrooted tree (shown) is virtually identical to the ML and NJ trees. Nodal support values ≥50 given as BI/ML/NJ. Asterisks (*) indicate support values <50. Scale bar indicates substitutions per site.

Figure 3. Physical maps of XP_001335286.1 in Danio rerio and its homologs distribution in fishes.

(a) Physical maps of XP_001335286.1 in D. rerio. Arrows denote gene orientation. (b) Phylogeny indicates the general relationship of these fishes based on the NCBI Taxonomy information. Red triangles indicate species that possess XP_001335286.1 homologs.

Figure 4. Features and expression of transferred gene in Danio rerio.

(a) Domains of transferred gene coding protein XP_001335286.1. (b) Tertiary structures of transferred gene modelled by SWISS- MODEL server. (c) Expression levels of transferred gene in D. rerio along with developmental stages. Normalized levels of expression were estimated by count of mapped reads to this gene per kilobase of sequence length per million library reads (RPKM). (d) GC content distribution of transferred gene. Red area indicates the density distribution of GC content for D. rerio mRNA. Blue and green lines indicate the GC content of transferred gene in D. rerio and putative donor, respectively.