@article{mallik_carlson_wcisel_fisk_yoder_dornburg_2023, title={A chromosome-level genome assembly of longnose gar, Lepisosteus osseus}, volume={4}, ISSN={["2160-1836"]}, url={https://doi.org/10.1093/g3journal/jkad095}, DOI={10.1093/g3journal/jkad095}, abstractNote={Abstract}, journal={G3-GENES GENOMES GENETICS}, author={Mallik, Rittika and Carlson, Kara B. and Wcisel, Dustin J. and Fisk, Michael and Yoder, Jeffrey A. and Dornburg, Alex}, editor={Whiteman, NEditor}, year={2023}, month={Apr} }
 @article{carlson_nguyen_wcisel_yoder_dornburg_2023, title={Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution}, volume={8}, ISSN={["1432-1211"]}, url={https://doi.org/10.1007/s00251-023-01315-7}, DOI={10.1007/s00251-023-01315-7}, abstractNote={Since its initial discovery over 50 years ago, understanding the evolution of the vertebrate RAG- mediated adaptive immune response has been a major area of research focus for comparative geneticists. However, how the evolutionary novelty of an adaptive immune response impacted the diversity of receptors associated with the innate immune response has received considerably less attention until recently. Here, we investigate the diversification of vertebrate toll-like receptors (TLRs), one of the most ancient and well conserved innate immune receptor families found across the Tree of Life, integrating genomic data that represent all major vertebrate lineages with new transcriptomic data from Polypteriformes, the earliest diverging ray-finned fish lineage. Our analyses reveal TLR sequences that reflect the 6 major TLR subfamilies, TLR1, TLR3, TLR4, TLR5, TLR7, and TLR11, and also currently unnamed, yet phylogenetically distinct TLR clades. We additionally recover evidence for a pulse of gene gain coincident with the rise of the RAG-mediated adaptive immune response in jawed vertebrates, followed by a period of rapid gene loss during the Cretaceous. These gene losses are primarily concentrated in marine teleost fish and synchronous with the mid Cretaceous anoxic event, a period of rapid extinction for marine species. Finally, we reveal a mismatch between phylogenetic placement and gene nomenclature for up to 50% of TLRs found in clades such as ray-finned fishes, cyclostomes, amphibians, and elasmobranchs. Collectively, these results provide an unparalleled perspective of TLR diversity and offer a ready framework for testing gene annotations in non-model species.}, journal={IMMUNOGENETICS}, author={Carlson, Kara B. and Nguyen, Cameron and Wcisel, Dustin J. and Yoder, Jeffrey A. and Dornburg, Alex}, year={2023}, month={Aug} }
 @article{wcisel_dornburg_mcconnell_hernandez_andrade_jong_litman_yoder_2022, title={A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors}, volume={7}, ISSN={["1432-1211"]}, url={https://doi.org/10.1007/s00251-022-01270-9}, DOI={10.1007/s00251-022-01270-9}, abstractNote={Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout, and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversity, thereby limiting our predictions for their evolutionary origin and function. In order to better understand the diversity of NILTs and their possible roles in immune function, we identified five NILT loci in the Atlantic salmon (Salmo salar) genome, defined 86 NILT Ig domains within a 3-Mbp region of zebrafish (Danio rerio) chromosome 1, and described 41 NILT Ig domains as part of an alternative haplotype for this same genomic region. We then identified transcripts encoded by 43 different NILT genes which reflect an unprecedented diversity of Ig domain sequences and combinations for a family of non-recombining receptors within a single species. Zebrafish NILTs include a sole putative activating receptor but extensive inhibitory and secreted forms as well as membrane-bound forms with no known signaling motifs. These results reveal a higher level of genetic complexity, interindividual variation, and sequence diversity for NILTs than previously described, suggesting that this gene family likely plays multiple roles in host immunity.}, journal={IMMUNOGENETICS}, author={Wcisel, Dustin J. and Dornburg, Alex and McConnell, Sean C. and Hernandez, Kyle M. and Andrade, Jorge and Jong, Jill L. O. and Litman, Gary W. and Yoder, Jeffrey A.}, year={2022}, month={Jul} }
 @article{carlson_wcisel_ackerman_romanet_christiansen_niemuth_williams_breen_stoskopf_dornburg_et al._2022, title={Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri}, volume={4}, ISSN={["1572-9737"]}, url={https://doi.org/10.1007/s10592-022-01444-8}, DOI={10.1007/s10592-022-01444-8}, abstractNote={Briefly considered extinct in the wild, the future of the Wyoming toad (Anaxyrus baxteri) continues to rely on captive breeding to supplement the wild population. Given its small natural geographic range and history of rapid population decline at least partly due to fungal disease, investigation of the diversity of key receptor families involved in the host immune response represents an important conservation need. Population decline may have reduced immunogenetic diversity sufficiently to increase the vulnerability of the species to infectious diseases. Here we use comparative transcriptomics to examine the diversity of toll-like receptors and major histocompatibility complex (MHC) sequences across three individual Wyoming toads. We find reduced diversity at MHC genes compared to bufonid species with a similar history of bottleneck events. Our data provide a foundation for future studies that seek to evaluate the genetic diversity of Wyoming toads, identify biomarkers for infectious disease outcomes, and guide breeding strategies to increase genomic variability and wild release successes.}, journal={CONSERVATION GENETICS}, author={Carlson, Kara B. and Wcisel, Dustin J. and Ackerman, Hayley D. and Romanet, Jessica and Christiansen, Emily F. and Niemuth, Jennifer N. and Williams, Christina and Breen, Matthew and Stoskopf, Michael K. and Dornburg, Alex and et al.}, year={2022}, month={Apr} }
 @article{wyatt_amin_bagley_wcisel_dush_yoder_nascone-yoder_2021, title={Single-minded 2 is required for left-right asymmetric stomach morphogenesis}, volume={148}, ISSN={["1477-9129"]}, DOI={10.1242/dev.199265}, abstractNote={ABSTRACT}, number={17}, journal={DEVELOPMENT}, author={Wyatt, Brent H. and Amin, Nirav M. and Bagley, Kristen and Wcisel, Dustin and Dush, Michael K. and Yoder, Jeffrey A. and Nascone-Yoder, Nanette M.}, year={2021}, month={Sep} }
 @article{thompson_hawkins_parey_wcisel_ota_kawasaki_funk_losilla_fitch_pan_et al._2021, title={The bowfin genome illuminates the developmental evolution of ray-finned fishes}, volume={8}, ISSN={["1546-1718"]}, DOI={10.1038/s41588-021-00914-y}, abstractNote={Abstract}, journal={NATURE GENETICS}, author={Thompson, Andrew W. and Hawkins, M. Brent and Parey, Elise and Wcisel, Dustin J. and Ota, Tatsuya and Kawasaki, Kazuhiko and Funk, Emily and Losilla, Mauricio and Fitch, Olivia E. and Pan, Qiaowei and et al.}, year={2021}, month={Aug} }
 @article{wcisel_ota_litman_yoder_2017, title={Spotted Gar and the Evolution of Innate Immune Receptors}, volume={328}, ISSN={1552-5007}, url={http://dx.doi.org/10.1002/jez.b.22738}, DOI={10.1002/jez.b.22738}, abstractNote={ABSTRACT}, number={7}, journal={Journal of Experimental Zoology Part B: Molecular and Developmental Evolution}, publisher={Wiley}, author={Wcisel, Dustin J. and Ota, Tatsuya and Litman, Gary W. and Yoder, Jeffrey A.}, year={2017}, month={May}, pages={666–684} }
 @article{mcconnell_hernandez_wcisel_kettleborough_stemple_yoder_andrade_de jong_2016, title={Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution}, volume={113}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1607602113}, DOI={10.1073/pnas.1607602113}, abstractNote={Significance}, number={34}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={McConnell, Sean C. and Hernandez, Kyle M. and Wcisel, Dustin J. and Kettleborough, Ross N. and Stemple, Derek L. and Yoder, Jeffrey A. and Andrade, Jorge and de Jong, Jill L. O.}, year={2016}, month={Aug}, pages={E5014–E5023} }
 @article{wcisel_yoder_2016, title={The confounding complexity of innate immune receptors within and between teleost species}, volume={53}, ISSN={1050-4648}, url={http://dx.doi.org/10.1016/j.fsi.2016.03.034}, DOI={10.1016/j.fsi.2016.03.034}, abstractNote={Teleost genomes encode multiple multigene families of immunoglobulin domain-containing innate immune receptors (IIIRs) with unknown function and no clear mammalian orthologs. However, the genomic organization of IIIR gene clusters and the structure and signaling motifs of the proteins they encode are similar to those of mammalian innate immune receptor families such as the killer cell immunoglobulin-like receptors (KIRs), leukocyte immunoglobulin-like receptors (LILRs), Fc receptors, triggering receptors expressed on myeloid cells (TREMs) and CD300s. Teleost IIIRs include novel immune-type receptors (NITRs); diverse immunoglobulin domain containing proteins (DICPs); polymeric immunoglobulin receptor-like proteins (PIGRLs); novel immunoglobulin-like transcripts (NILTs) and leukocyte immune-type receptors (LITRs). The accumulation of genomic sequence data has revealed that IIIR gene clusters in zebrafish display haplotypic and gene content variation. This intraspecific genetic variation, as well as significant interspecific variation, frequently confounds the identification of definitive orthologous IIIR sequences between teleost species. Nevertheless, by defining which teleost lineages encode (and do not encode) different IIIR families, predictions can be made about the presence (or absence) of specific IIIR families in each teleost lineage. It is anticipated that further investigations into available genomic resources and the sequencing of a variety of multiple teleost genomes will identify additional IIIR families and permit the modeling of the evolutionary origins of IIIRs.}, journal={Fish & Shellfish Immunology}, publisher={Elsevier BV}, author={Wcisel, Dustin J. and Yoder, Jeffrey A.}, year={2016}, month={Jun}, pages={24–34} }
 @article{rodriguez-nunez_wcisel_litman_litman_yoder_immunogenetics_2016, title={The identification of additional zebrafish DICP genes reveals haplotype variation and linkage to MHC class I genes}, volume={68}, ISSN={0093-7711 1432-1211}, url={http://dx.doi.org/10.1007/s00251-016-0901-6}, DOI={10.1007/s00251-016-0901-6}, abstractNote={Bony fish encode multiple multi-gene families of membrane receptors that are comprised of immunoglobulin (Ig) domains and are predicted to function in innate immunity. One of these families, the diverse immunoglobulin (Ig) domain-containing protein (DICP) genes, maps to three chromosomal loci in zebrafish. Most DICPs possess one or two Ig ectodomains and include membrane-bound and secreted forms. Membrane-bound DICPs include putative inhibitory and activating receptors. Recombinant DICP Ig domains bind lipids with varying specificity, a characteristic shared with mammalian CD300 and TREM family members. Numerous DICP transcripts amplified from different lines of zebrafish did not match the zebrafish reference genome sequence suggesting polymorphic and haplotypic variation. The expression of DICPs in three different lines of zebrafish has been characterized employing PCR-based strategies. Certain DICPs exhibit restricted expression in adult tissues whereas others are expressed ubiquitously. Transcripts of a subset of DICPs can be detected during embryonic development suggesting roles in embryonic immunity or other developmental processes. Transcripts representing 11 previously uncharacterized DICP sequences were identified. The assignment of two of these sequences to an unplaced genomic scaffold resulted in the identification of an alternative DICP haplotype that is linked to a MHC class I Z lineage haplotype on zebrafish chromosome 3. The linkage of DICP and MHC class I genes also is observable in the genomes of the related grass carp (Ctenopharyngodon idellus) and common carp (Cyprinus carpio) suggesting that this is a shared character with the last common Cyprinidae ancestor.}, number={4}, journal={Immunogenetics}, publisher={Springer Science and Business Media LLC}, author={Rodriguez-Nunez, I. and Wcisel, D.J. and Litman, R.T. and Litman, G.W. and Yoder, J.A. and Immunogenetics}, year={2016}, month={Jan}, pages={295–312} }
 @article{braasch_gehrke_smith_kawasaki_manousaki_pasquier_amores_desvignes_batzel_catchen_et al._2016, title={The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons}, volume={48}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/ng.3526}, DOI={10.1038/ng.3526}, abstractNote={To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.}, number={4}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Braasch, Ingo and Gehrke, Andrew R and Smith, Jeramiah J and Kawasaki, Kazuhiko and Manousaki, Tereza and Pasquier, Jeremy and Amores, Angel and Desvignes, Thomas and Batzel, Peter and Catchen, Julian and et al.}, year={2016}, month={Mar}, pages={427–437} }
 @article{rodríguez-nunez_wcisel_litman_yoder_2014, title={Multigene families of immunoglobulin domain-containing innate immune receptors in zebrafish: Deciphering the differences}, volume={46}, ISSN={0145-305X}, url={http://dx.doi.org/10.1016/j.dci.2014.02.004}, DOI={10.1016/j.dci.2014.02.004}, abstractNote={Five large multigene families encoding innate-type immune receptors that are comprised of immunoglobulin domains have been identified in bony fish, of which four do not possess definable mammalian orthologs. The members of some of the multigene families exhibit unusually extensive patterns of divergence and the individual family members demonstrate marked variation in interspecific comparisons. As a group, the gene families reveal striking differences in domain type and content, mechanisms of intracellular signaling, basic structural features, haplotype and allelic variation and ligand binding. The potential functional roles of these innate immune receptors, their relationships to immune genes in higher vertebrate species and the basis for their adaptive evolution are of broad interest. Ongoing investigations are expected to provide new insight into alternative mechanisms of immunity.}, number={1}, journal={Developmental & Comparative Immunology}, publisher={Elsevier BV}, author={Rodríguez-Nunez, Iván and Wcisel, Dustin J. and Litman, Gary W. and Yoder, Jeffrey A.}, year={2014}, month={Sep}, pages={24–34} }