GigaByte (Jan 2024)
Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)
- Magnus Wolf ,
- Bruno Lopes da Silva Ferrette ,
- Raphael T. F. Coimbra ,
- Menno de Jong ,
- Marcel Nebenführ ,
- David Prochotta ,
- Yannis Schöneberg ,
- Konstantin Zapf ,
- Jessica Rosenbaum ,
- Hannah A. Mc Intyre ,
- Julia Maier ,
- Clara C. S. de Souza ,
- Lucas M. Gehlhaar ,
- Melina J. Werner ,
- Henrik Oechler ,
- Marie Wittekind ,
- Moritz Sonnewald ,
- Maria A. Nilsson ,
- Axel Janke ,
- Sven Winter
Affiliations
- Magnus Wolf
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Bruno Lopes da Silva Ferrette
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Raphael T. F. Coimbra
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Menno de Jong
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Marcel Nebenführ
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- David Prochotta
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Yannis Schöneberg
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Konstantin Zapf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Jessica Rosenbaum
- ORCiD
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Hannah A. Mc Intyre
- ORCiD
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Julia Maier
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Clara C. S. de Souza
- ORCiD
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Lucas M. Gehlhaar
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Melina J. Werner
- ORCiD
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Henrik Oechler
- ORCiD
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Marie Wittekind
- ORCiD
- Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany
- Moritz Sonnewald
- ORCiD
- Senckenberg Research Institute, Department of Marine Zoology, Section Ichthyology, Frankfurt am Main, Germany
- Maria A. Nilsson
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, LOEWE-Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- Axel Janke
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany, LOEWE-Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
- Sven Winter
- ORCiD
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany, Institute for Ecology, Evolution, and Diversity, Goethe University, Frankfurt am Main, Germany, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
Abstract
The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a northern Atlantic fish inhabiting open seagrass environments that recently expanded its distribution range. Here, we present a highly contiguous, near chromosome-scale genome of E. aequoreus. The final assembly spans 1.6 Gbp in 7,391 scaffolds, with a scaffold N50 of 62.3 Mbp and L50 of 12. The 28 largest scaffolds (>21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions identified in vertebrates. Our demographic modeling identified a peak in population size during the last interglacial period, suggesting the species might benefit from warmer water conditions. Our updated snake pipefish assembly is essential for future analyses of the morphological and molecular changes unique to the Syngnathidae.
