Evolutionary innovation through fusion of sequences from across the tree of life

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 interaction of HGT with other mechanisms of novel gene formation 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 19 arthropod species predicted to harbor HGT-chimeras in their genome. We found evidence of the expression of contiguous chimeric mRNAs for 33 of 37 tested HGT-chimeras across 17 of 19 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.