Phylogenomic Studies on the Evolution of Morphological Complexity

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The study of our most distant animal relatives through the use of phylogenetic and comparative genomic approaches has significantly advanced our understanding of the relationship between genomic and morphological complexity, the evolution of multicellularity, and the emergence of novel cell types. These findings are leading to the establishment of new model organisms that have the potential to inform important questions in human biology and human health, laying the groundwork for translational studies focused on specific human diseases. The cnidarians, organisms unified in a single phylum based on their use of cnidocytes to capture prey and for defense from predators, occupy a key phylogenetic position as the sister group to the bilaterians. Previous phylogenomic analyses performed by our group have revealed that the genomes of cnidarians encode more homologs to human disease genes than do classic invertebrate models (1), strongly positioning the cnidarians as powerful model systems for the study of biological processes such as pluripotency, regeneration, lineage commitment, and allorecognition. Given their experimental tractability, including the ability to perform CRISPR/Cas9-mediated gene knock-ins (2), we are actively sequencing and annotating the genomes of two Hydractinia species: H. echinata and H. symbiolongicarpus. What makes these simple organisms particularly well-suited as a model system lies in the fact that they possess a specific type of interstitial cell (or i-cell) that is pluripotent and provides the basis for tissue regeneration, expressing genes whose bilateral homologs are known to be involved in stem cell biology. Hydractinia is also colonial, possessing an allorecognition system that may provide insights into important questions related to host-graft rejection. Using PacBio, Illumina, and Dovetail-based strategies, high-coverage sequencing data indicate an estimated genome size of 774 Mb for H. echinata (84x coverage) and 514 Mb for H. symbiolongicarpus (94x coverage); these genomes are AT-rich (65%) and highly repetitive (47-51%). The N50 for the H. symbiolongicarpus genome exceeds 2.2 MB, making this one of the most contiguous animal genomes sequenced to date. The vast majority of a set of evolutionarily conserved single-copy orthologs can be easily identified in these assemblies, and analyses of these whole-genome sequencing data have already provided important insights into the evolution of chromatin compaction (3) and metazoan neurogenesis (4). Allorecognition. The analysis of these Hydractinia genomes has also revealed a heretofore unappreciated complexity of the mechanisms underlying allorecognition. Previously, it was thought that two genes (named Alr1 and Alr2) found within the allorecognition complex (ARC) controlled the ability of colonies to distinguish self from non-self through potential signal transduction motifs in their extracellular domains. Analysis of our highly contiguous whole-genome sequence data has revealed there are 10 putative Alr genes located within the 12 Mb allorecognition complex, with fusion assays indicating that Alr4 is a putative third allodeterminant (manuscript in preparation). The genomic architecture of the ARC is similar to that of mammalian natural killer cell receptors that also exhibit high levels of allelic polymorphism, gene duplication, and copy number variation, suggesting common mechanisms of genomic evolution in both systems. Germ Cell Induction. Clonal animals such as Hydractinia do not sequester a germline during embryogenesis, instead producing gametes from adult stem cells that can also contribute to somatic tissues. However, how germ fate is induced in these animals and whether this process is related to bilateral embryonic germline induction remains an open question. Along with our collaborators at the University of Ireland-Galway, we have shown that transcription factor AP2 (Tfap2), a major regulator of mammalian germline induction, acts as a molecular switch that commits i-cells to germ fate in Hydractinia. Tfap2 mutants were shown to lack germ cells, developing only rudimentary gonads, while transplanted allogenic wild-type cells rescued gonad development but not germ cell induction in Tfap2 mutants. Further, forced expression of Tfap2 in i-cells converted them to germ cells ectopically in non-gonadal tissues of embryos and juveniles, but Tfap2 expression produced no discernible phenotype in somatic cells. These data show that Tfap2 acts cell-autonomously and is essential and sufficient to induce germ cell fate in i-cells, also acting non-cell-autonomously downstream of germ cell induction to promote gonad development. Therefore, Tfap2 is a conserved regulator of germ cell commitment across germline-sequestering and germline-non-sequestering animals (5). Data Sharing. Given the increased emphasis on the development of new animal models for the study of human health, it is extremely important that genomic data generated using these emerging research organisms be disseminated to the biomedical research community in as accessible a fashion as possible. To facilitate access to and use of the data generated during the course of our sequencing, assembly, and annotation efforts, we have developed the Hydractinia Genome Project Portal, located at https://research.nhgri.nih.gov/hydractinia. The scope of data available through the Portal goes well-beyond the sequence data available through GenBank, providing additional biological information intended to increase the utility of the sequencing data generated by our group. It also provides a customized, interactive JBrowse front-end for visualizing assemblies, gene predictions, assembled, transcripts, predicted functional domains, non-coding RNA sequences, and methylation data from both species. The structure of the database parallels that of the Mnemiopsis Genome Project Portal (6), a research organism database that we originally developed in 2013 (and significantly expanded in 2020) as a straightforward model whose design places a premium on usability, intuitive navigation, and clarity, as well as providing easy access to value-added data that is not available elsewhere. Finally, in a collaboration with Brant Weinstein (NICHD/DIR), we profiled the gene expression patterns of undisturbed endothelial cells in living animals using a novel AngioTag zebrafish transgenic line that permits isolation of actively translating mRNAs from endothelial cells in their native environment (7). This transgenic line uses the endothelial cell-specific kdrl promoter to drive expression of an epitope-tagged Rpl10a 60S ribosomal subunit progein, allowing for Translating Ribosome Affinity Purification (TRAP) of actively translating endothelial cell mRNAs. TRAP-RNAseq on AngioTag animals indicated strong enrichment of endothelial-specific genes and uncovered novel endothelially expressed genes. Additionally, UAS:RiboTag transgenic lines were generated to allow for the study of a wider array of zebrafish cell and tissue types using TRAP-RNAseq methods. This new tool offers an unparalleled resource to study cause and effect relationships in the context of gene loss or gain of function in vivo. (1) Maxwell, E.K. et al. BMC Evolutionary Biology 14: 212, 2014 (2) Sanders, S.M. et al. BMC Genomics 19: 649, 2018 (3) Trk, A. et al., Epigenetics & Chromatin 9: 36, 2016 (4) Gahan, J.M. et al., Dev. Biol. 428: 224-231, 2017 (5) DuBuc, T.Q. et al., Science 367: 757-762, 2020 (6) Moreland, R.T. et al., Database (Oxford) 1-9 (doi:10.1093/database/baaa029), 2020 (7) Miller, M. et al., BioRxiv (doi:10.1101/815696), 2019