Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta

Abstract

Horizontal gene transfer (HGT), the movement of heritable materials between distantly related organisms, is crucial in eukaryotic evolution. However, the scale of HGT in choanoflagellates, the closest unicellular relatives of metazoans, and its possible roles in the evolution of animal multicellularity remains unexplored. We identified at least 175 candidate HGTs in the genome of the colonial choanoflagellate Salpingoeca rosetta using sequence-based tests. The majority of these were orthologous to genes in bacterial and microalgal lineages, yet displayed genomic features consistent with the rest of the S. rosetta genome-evidence of ancient acquisition events. Putative functions include enzymes involved in amino acid and carbohydrate metabolism, cell signaling, and the synthesis of extracellular matrix components. Functions of candidate HGTs may have contributed to the ability of choanoflagellates to assimilate novel metabolites, thereby supporting adaptation, survival in diverse ecological niches, and response to external cues that are possibly critical in the evolution of multicellularity in choanoflagellates.

Figure 1

HGT candidates in the S. rosetta genome. (A) Taxonomic affiliation of all S. rosetta genes and genes that passed the Alien Index analysis (AI45). (B) Number of putative HGTs detected based on taxonomic affiliation (taxon filter) and Alien Index (AI45) analysis. (C) Number of HGT candidates with orthologs in other eukaryotic lineages.

Figure 2

Gene architecture of candidate HGTs. Density plots showing the distribution of (A) coding sequence length, (B) GC content at the third codon position (GC3), (C) intron number, and (D) codon bias index in candidate horizontally transferred genes (red) in comparison to the bulk of S. rosetta genes (gray). (E) Number of HGT candidates that are expressed in the indicated life stages of S. rosetta. (F) Number of HGT candidates conserved in other choanoflagellate groups.

Figure 3

Potential donor phyla of candidate HGTs in S. rosetta. (A) Taxon affiliation of candidate HGTs based on the best sequence match for each gene. Phylogenetic analysis of selected candidate HGTs, including (B) calcium binding protein of microalgal origin, (C) glycosyltransferase of fungal origin, and (D) chondroitin sulfate lyase, (E) glycosyl hydrolase, and (F) diaminopimelate epimerase of prokaryotic origin. Genes from choanoflagellates are shown in red, fungi or opisthokonts in orange, microalgae in green, and prokaryotes in blue. S. rosetta genes are indicated by a red dot. Trees were generated using MrBayes 3.2.6. Circles at the branches indicate posterior probabilities of 0.70–1.00.

Figure 4

Functional analysis of candidate HGTs. (A) Most common PFAM protein domains in the set of candidate HGTs. (B) Gene ontology functions enriched in the set of putative HGTs. Enrichment p-values (p ≤ 0.05) for selected functions are shown. (C) Number of candidate HGTs with associated functions based on manual curation.