Rishabh R. Kapoor

Horizontal gene transfer (HGT) in animals is thought to be rare and largely restricted to transfers from non-animal sources. In contrast to this expectation, we discovered that 9.2% of the protein-coding genes in the genome of the dark-winged fungus gnat Bradysia coprophila (order: Diptera, family: Sciaridae) are of potential HGT origin. Most of these genes have phylogenetic affinity with sequences from other distantly related arthropods that inhabit a shared soil-dwelling niche with B. coprophila. We show that these findings are inconsistent with genomic contamination or widespread gene loss and instead suggest a level of inter-animal HGT that is, to our knowledge, unprecedented. Consistent with their potential functional importance, ~75% of putative B. coprophila horizontally transferred genes (HTGs) are transcribed, and nearly all are shared across multiple sciarid fungus gnat species that diverged tens of millions of years ago. Further, domain annotations suggest that HTGs participate in diverse processes potentially important to B. coprophila ecology. We tested the functions of eight putative B. coprophila HTGs through transgenic expression in the fly Drosophila melanogaster and the yeast Saccharomyces cerevisiae, and found evidence that HGT has likely endowed B. coprophila with the novel capability to biosynthesize NAD+, as well as enhanced capacity to withstand stressors imposed by arsenic, cyanide, alkylating agents, and reactive oxygen species. Our findings reveal a previously underappreciated contribution of inter-animal genetic exchange to the evolution of genomic, physiological, and ecological novelty.

Novel genes arise through multiple mechanisms, including gene duplication, gene fusion, and horizontal gene transfer (HGT). While HGT has increasingly been documented in animals, the posttransfer evolutionary fate of horizontally acquired genes is less well understood. We hypothesized that fusion with endogenous sequences in animal genomes might generate what we call “HGT-chimeras”: genes with regions of nonmetazoan and metazoan descent in the same open reading frame. To test this hypothesis, we developed a molecular phylogenetics pipeline that enables the identification of HGT-chimeras. We applied our pipeline to 319 high-quality annotated arthropod genomes and uncovered a high-confidence set of 274 HGT-chimeras corresponding to 104 independent origination events across diverse arthropods. HGT-chimeras contain intervals acquired from across the tree of life, and many likely originated via a gene duplication-based mechanism. To assess whether HGT-chimeras might be functionally important, we performed RT-PCR and Sanger sequencing of tissues from 20 arthropod species predicted to harbor HGT-chimeras in their genome. We found evidence for the expression of contiguous chimeric messenger RNA transcripts (mRNAs) for 36 of 41 tested HGT-chimeras across 18 of 20 different tested species. We also found evidence that HGT-chimeras evolve under purifying selection and have acquired potentially functional domain architectures, consistent with the hypothesis that these genes are in active use and may participate in diverse biological processes. These results illuminate an underappreciated combinatorial mechanism underlying the origin of novel genes across the largest animal phylum, and suggest that interdomain sequence fusion can play important roles in animal biology and evolution.

Germ cells enable the reproduction of an organism and the continuity of its lineage. Across animals, these crucial cells are segregated from the soma at different times and places and via distinct mechanisms. Understanding the evolution of germ cell specification across animals is complicated by the difficulty of making meaningful comparisons of embryonic development between diverse animal species. Here, we characterize germ cell specification in Panarthropoda, an ancient clade that encompasses massive animal biodiversity, within which we can conduct meaningful comparative embryology. We amass data from centuries of studies describing the timing and mechanisms of germ cell formation, and apply ancestral state reconstruction to these data to propose hypotheses about the trajectory of evolution in this process. Furthermore, we speculate about the mechanisms underlying these evolutionary dynamics by considering the relationships among germ cell specification, concurrent developmental processes and the germ line gene network. Collectively, this Review derives new insights from a rich historical database of embryological observations, offering broad implications for understanding the evolution of metazoan germ cells.

Novel genes arise through multiple mechanisms, including gene duplication, gene fusion and horizontal gene transfer (HGT). While HGT has increasingly been documented in animals, the post-transfer evolutionary fate of horizontally-acquired genes is less well understood. We hypothesized that fusion with endogenous sequences in animal genomes might generate what we call “HGT-chimeras”: genes with regions of non-metazoan and metazoan descent in the same open reading frame. To test this hypothesis, we developed a molecular phylogenetics pipeline that enables the identification of HGT-chimeras. We applied our pipeline to 319 high-quality annotated arthropod genomes and uncovered a high-confidence set of 274 HGT-chimeras corresponding to 104 independent origination events across diverse arthropods. HGT-chimeras contain intervals acquired from across the tree of life, and many likely originated via a gene duplication-based mechanism. To assess whether HGT-chimeras might be functionally important, we performed RT-PCR and Sanger sequencing of tissues from 20 arthropod species predicted to harbor HGT-chimeras in their genome. We found evidence for the expression of contiguous chimeric mRNAs for 36 of 41 tested HGT-chimeras across 18 of 20 different tested species. We also found evidence that HGT chimeras evolve under purifying selection and have acquired potentially functional domain architectures, consistent with the hypothesis that these genes are in active use and may participate in diverse biological processes. These results illuminate an underappreciated combinatorial mechanism underlying the origin of novel genes across the largest animal phylum, and suggest that interdomain sequence fusion can play important roles in animal biology and evolution. Significance: Evolution forges novelty through the repurposing of available parts. Can recently acquired parts, previously foreign to an organism, be similarly repurposed? Applying a rigorous methodology to 319 genomes from arthropods, the largest phylum of animals, we uncover 104 novel genes that arose from the fusion of animal genes with fragments acquired via horizontal gene transfer from bacteria, viruses, fungi, and plants. RNA-Seq and RT-PCR across multiple species show that many of these novel genes are expressed as mRNAs. Many show signatures of evolutionary conservation and coherent domain architectures, suggesting that these chimeric genes may play important roles in diverse biological processes. These results reveal an understudied path to evolutionary innovation via “bricolage” of genes from across the tree of life.

Germ cells enable the reproduction of an organism and the continuity of its lineage. Across animals, these crucial cells are segregated from the soma at different times and places and via distinct mechanisms. Understanding the evolution of germ cell specification across animals is complicated by the difficulty of making meaningful comparisons of embryonic development between diverse animal species. Here, we characterize germ cell specification in Panarthropoda, an ancient clade that encompasses massive animal biodiversity, within which we can conduct meaningful comparative embryology. We amass data from centuries of studies describing the timing and mechanisms of germ cell formation, and apply ancestral state reconstruction to these data to propose novel hypotheses about the trajectory of evolution in this process. Furthermore, we speculate about the mechanisms underlying these evolutionary dynamics by considering the relationships among germ cell specification, concurrent developmental processes and the germ line gene network. Collectively, this Review derives new insights from a rich historical database of embryological observations, offering broad implications for understanding the evolution of metazoan germ cells.