Near chromosome-level and highly repetitive genome assembly of the snake pipefish Entelurus aequoreus (Syngnathiformes: Syngnathidae)

  • The snake pipefish, Entelurus aequoreus (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university master’s course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 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 so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 – 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.

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Metadaten
Author:Magnus WolfORCiDGND, Bruno Lopes da Silva FerretteORCiD, Raphael T. F. CoimbraORCiD, Menno de JongORCiD, Marcel NebenführORCiD, David ProchottaORCiD, Yannis SchönebergORCiD, Konstantin ZapfORCiD, Jessica RosenbaumORCiD, Hannah A. Mc IntyreORCiD, Julia Maier, Clara Cavalcanti Salomão de SouzaORCiD, Lucas M. Gehlhaar, Melina J. WernerORCiD, Henrik OechlerORCiD, Marie WittekindORCiD, Moritz SonnewaldORCiDGND, Maria A. NilssonORCiD, Axel JankeORCiD, Sven WinterORCiDGND
URN:urn:nbn:de:hebis:30:3-830245
URL:https://www.biorxiv.org/content/10.1101/2023.12.12.571260v1
DOI:https://doi.org/10.1101/2023.12.12.571260
Parent Title (English):bioRxiv
Publisher:bioRxiv
Document Type:Preprint
Language:English
Date of Publication (online):2023/12/13
Date of first Publication:2023/12/13
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2024/04/09
Issue:2023.12.12.571260 Version 1
Edition:Version 1
Page Number:20
HeBIS-PPN:517299119
Institutes:Angeschlossene und kooperierende Institutionen / Senckenbergische Naturforschende Gesellschaft
Biowissenschaften / Institut für Ökologie, Evolution und Diversität
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 59 Tiere (Zoologie) / 590 Tiere (Zoologie)
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - CC BY-NC - Namensnennung - Nicht kommerziell 4.0 International