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

GigaByte (Hong Kong, China) Pub Date : 2024-01-11 eCollection Date: 2024-01-01 DOI:10.46471/gigabyte.105

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

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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.

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蛇琵琶鱼 Entelurus aequoreus (Syngnathiformes: Syngnathidae) 的近染色体水平和高度重复基因组组装。

蛇琵琶鱼（Entelurus aequoreus，Linnaeus，1758 年）是一种栖息于开阔海草环境中的大西洋北部鱼类，最近其分布范围有所扩大。在这里，我们展示了一个高度连续、接近染色体尺度的 E. aequoreus 基因组。最终的组装跨越 1.6 Gbp，包含 7,391 个支架，支架 N50 为 62.3 Mbp，L50 为 12。最大的 28 个支架（>21 Mbp）占组装长度的 89.7%。BUSCO 完整性得分为 94.1%，映射率超过 98%，表明组装的完整性很高。重复元件覆盖了基因组的 74.93%，是脊椎动物中发现的最高比例之一。我们的人口统计建模确定了上一个冰期的种群数量高峰，这表明该物种可能受益于较温暖的水域条件。我们更新的蛇琵琶鱼基因组对于未来分析蛇琵琶鱼科特有的形态和分子变化至关重要。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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