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Horizontal gene transfer events have played a major role in the evolution of microbial species, but their importance in animals is less clear. Here, we report horizontal gene transfer of cytolethal distending toxin B (cdtB), prokaryotic genes encoding eukaryote-targeting DNase I toxins, into the genomes of vinegar flies (Diptera: Drosophilidae) and aphids (Hemiptera: Aphididae). We found insect-encoded cdtB genes are most closely related to orthologs from bacteriophage that infect Candidatus Hamiltonella defensa, a bacterial mutualistic symbiont of aphids that confers resistance to parasitoid wasps. In drosophilids, cdtB orthologs are highly expressed during the parasitoid-prone larval stage and encode a protein with ancestral DNase activity. We show that cdtB has been domesticated by diverse insects and hypothesize that it functions in defense against their natural enemies., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Horizontal gene transfer (HGT) is believed to shape genomes by facilitating the rapid acquisition of adaptive traits. We hypothesized that the economically important fungus Fusarium verticillioides is an excellent candidate for investigating the potential impact of HGT on the expansion of metabolic activities given its soilborne nature and versatile lifestyle as both a symptomless endophyte as well as a maize pathogen. To test this hypothesis, we used a phylogenomic pipeline followed by manual curation to perform a genome-wide identification of inter-kingdom derived HGT events. We found strong support for 36 genes in F. verticillioides putatively acquired from bacteria. Functional enrichment assessment of these 36 candidates suggested HGT potentially influenced several biochemical activities, including lysine, glycine and nitrogen metabolism. The expression of 25 candidate HGT genes was detected among RNA-Seq datasets from normal and various stress-related growth conditions, thus indicating potential functionality. FVEG_10494, one of the HGT candidates with homologs in only a few Fusarium species, was highly and specifically up-regulated under nitric oxide (NO) challenge. Functional analysis of FVEG_10494 suggests the gene moderately enhanced NO-triggered protective responses and suppressed expression of the F. verticillioides secondary metabolism gene cluster responsible for production of fusarin C. Overall, our global analysis of HGT events in F. verticillioides identified a well-supported set of transferred genes, providing further evidence that HGT offers a mechanism by which fungi can expand their metabolic capabilities, which in turn may enhance their adaptive strategies., (Published by Elsevier Inc.)

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. Here, we show that in a yeast lineage (the Wickerhamiella / Starmerella , W/S clade) comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodeling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene. An enzyme required for sucrose assimilation was also acquired from bacteria, suggesting that the genetic novelties identified in the W/S clade may be related to adaptation to the high-sugar environment. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events., Competing Interests: CG, JW, JK, MO, ML, XS, DO, XZ, DP, CK, CH, AR, PG No competing interests declared, (© 2018, Gonçalves et al.)

Horizontal gene transfer (HGT) among bacteria, archaea, and viruses is widespread, but the extent of transfers from these lineages into eukaryotic organisms is contentious. Here we systematically identify hundreds of genes that were likely acquired horizontally from a variety of sources by the early-diverging fungal phyla Microsporidia and Cryptomycota. Interestingly, the Microsporidia have acquired via HGT several genes involved in nucleic acid synthesis and salvage, such as those encoding thymidine kinase (TK), cytidylate kinase, and purine nucleotide phosphorylase. We show that these HGT-derived nucleic acid synthesis genes tend to function at the interface between the metabolic networks of the host and pathogen. Thus, these genes likely play vital roles in diversifying the useable nucleic acid components available to the intracellular parasite, often through the direct capture of resources from the host. Using an in vivo viability assay, we also demonstrate that one of these genes, TK, encodes an enzyme that is capable of activating known prodrugs to their active form, which suggests a possible treatment route for microsporidiosis. We further argue that interfacial genes with well-understood activities, especially those horizontally transferred from bacteria or viruses, could provide medical treatments for microsporidian infections.

Phylomes (comprehensive sets of gene phylogenies for organisms) are built to investigate fundamental questions in genomics and evolutionary biology, such as those pertaining to the detection and characterization of horizontal gene transfer in microbes. To address these questions, phylome construction demands rigorous yet efficient phylogenetic methods. Currently, many sequence alignment and tree-building models can analyze several thousands of genes in a high-throughput manner. However, the phylogenetics is complicated by variability in sequence divergence and different taxon sampling among genes. In addition, homolog selection for automated approaches often relies on arbitrary sequence similarity thresholds that are likely inappropriate for all genes in a genome. To investigate the effects of automated homolog selection on the detection of horizontal gene transfer using phylogenomics, we constructed the phylome of a transcriptome assembly of Alexandrium tamarense, a microbial eukaryote with a history of horizontal and endosymbiotic gene transfer, using seven sequence similarity thresholds for selecting putative homologs to be included in phylogenetic analyses. We show that no single threshold recovered informative trees for the majority of A. tamarense unigenes compared to the pooled results from all pipeline iterations. As much as 29% of trees built could have misleading phylogenetic relationships that appear biased in favor of those otherwise indicative of horizontal gene transfer. Perhaps worse, nearly half of the unigenes were represented by a single tree built at just one threshold, making it difficult to assess the validity of phylogenetic relationships recovered in these cases. However, combining the results from several pipeline iterations maximizes the number of informative phylogenies. Moreover, when the same phylogenetic relationship for a given unigene is recovered in multiple pipeline iterations, conclusions regarding gene origin are more robust to methodological artifact. Using these methods, the majority of A. tamarense unigenes showed evolutionary relationships indicative of vertical inheritance. Nevertheless, many other unigenes revealed diverse phylogenetic associations, suggestive of possible gene transfer. This analysis suggests that caution should be used when interpreting the results from phylogenetic pipelines implementing a single similarity threshold. Our approach is a practical method to mitigate the problems associated with automated sequence selection in phylogenomics., (Copyright © 2013 Elsevier Inc. All rights reserved.)

The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314-1,563 depending on inference method) relative to all other organisms in the analysis (0-782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.