@article{3fcf989fbb78455b9b2ab49c45b682d8,
title = "Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes",
abstract = "Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations of evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent noncoding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve reorganization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and hold value for conservation of the extravagant seadragons and their relatives.",
keywords = "fibroblast growth factors, genome sequencing, novel traits, syngnathid fishes, transposable elements",
author = "Small, {Clayton M.} and Healey, {Hope M.} and Currey, {Mark C.} and Beck, {Emily A.} and Julian Catchen and Lin, {Angela S.P.} and Cresko, {William A.} and Susan Bassham",
note = "Funding Information: ACKNOWLEDGMENTS. We are truly grateful for the dedicated efforts of L. Mat-sushige and the seadragon husbandry staff of the Birch Aquarium at Scripps Institution of Oceanography, who preserved P. eques samples crucial for this work. We also thank the Tennessee Aquarium, and particularly Aquarist K. Hurt for generous sharing of P. taeniolatus samples. We are indebted to M. Weitzman and D. Turnbull from the University of Oregon (UO) GC3F for critical assistance with library preparation and sequencing. We would like to acknowledge staff at Carl Zeiss Microscopy, LLC, particularly J. Mancuso, A. Browning, K. Skinner, and R. White for collaborating to scan the Gulf pipefish in SI Appendix, Fig. S2. We thank E. Reister and staff at Phase Genomics for helpful Hi-C technical support. We are grateful to T. Desvignes for guidance on the miRNA annotations. We especially thank C. Kimmel for his helpful comments on the manuscript. This work was funded by NIH Grants RR032670 and P50GM098911 (to W.A.C.), NSF Grant OPP-2015301 (to C.M.S., S.B., and W.A.C.), and Oregon Research Excellence Funds (to W.A.C.). H.M.H. was supported by the Genetics Training Program (NIH T32GM007413) at UO. Purchase of the Zeiss Xradia 620 Versa at UO was funded by an M. J. Murdock Charitable Trust Grant SR-201812008 (to W.A.C.). Funding Information: We are truly grateful for the dedicated efforts of L. Matsushige and the seadragon husbandry staff of the Birch Aquarium at Scripps Institution of Oceanography, who preserved P. eques samples crucial for this work. We also thank the Tennessee Aquarium, and particularly Aquarist K. Hurt for generous sharing of P. taeniolatus samples. We are indebted to M. Weitzman and D. Turnbull from the University of Oregon (UO) GC3F for critical assistance with library preparation and sequencing. We would like to acknowledge staff at Carl Zeiss Microscopy, LLC, particularly J. Mancuso, A. Browning, K. Skinner, and R. White for collaborating to scan the Gulf pipefish in SI Appendix, Fig. S2. We thank E. Reister and staff at Phase Genomics for helpful Hi-C technical support. We are grateful to T. Desvignes for guidance on the miRNA annotations. We especially thank C. Kimmel for his helpful comments on the manuscript. This work was funded by NIH Grants RR032670 and P50GM098911 (to W.A.C.), NSF Grant OPP-2015301 (to C.M.S., S.B., and W.A.C.), and Oregon Research Excellence Funds (to W.A.C.). H.M.H. was supported by the Genetics Training Program (NIH T32GM007413) at UO. Purchase of the Zeiss Xradia 620 Versa at UO was funded by an M. J. Murdock Charitable Trust Grant SR-201812008 (to W.A.C.). Publisher Copyright: Copyright {\textcopyright} 2022 the Author(s).",
year = "2022",
month = jun,
day = "28",
doi = "10.1073/pnas.2119602119",
language = "English (US)",
volume = "119",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
publisher = "National Academy of Sciences",
number = "26",
}