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<p>The sand martin (<i>Riparia riparia</i>), a widely distributed migratory songbird, is a promising model for evolutionary and population genetics due to its unique life-history traits. It also provides a valuable system for studying germline-restricted chromosome (GRC) inheritance and evolution. However, the absence of a high-quality genomic resource has limited in-depth investigation of these phenomena. Here, we present a chromosome-level somatic genome assembly for a <i>R. riparia</i> male generated using PacBio HiFi long-read sequencing and Hi-C scaffolding. The pseudohaploid assembly spans 1.19 Gb across 40 chromosome models and shows high completeness (97.6% BUSCO score). Repetitive elements make up 20.2% of the assembled chromosomes. A total of 19,624 protein-coding genes were annotated by integrating transcriptome evidence, <i>ab initio</i> gene prediction, and homology-based approaches. This high-quality reference genome provides a valuable foundation for studying population structure, adaptation, and evolutionary history in <i>R. riparia</i>. It serves as a critical resource for future assembly and investigation of the GRC, and contributes to a broader understanding of genome evolution in birds.</p>

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Chromosome-level genome assembly of the sand martin (Riparia riparia)

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月7日

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  • Miroslav Nuriddinov,
  • Lyubov Malinovskaya,
  • Aleksandr Bobrovskikh,
  • Maria Gridina,
  • Natalya A. Serdyukova,
  • Alexander Suh,
  • Francisco J. Ruiz-Ruano,
  • Anna Torgasheva

摘要

The sand martin (Riparia riparia), a widely distributed migratory songbird, is a promising model for evolutionary and population genetics due to its unique life-history traits. It also provides a valuable system for studying germline-restricted chromosome (GRC) inheritance and evolution. However, the absence of a high-quality genomic resource has limited in-depth investigation of these phenomena. Here, we present a chromosome-level somatic genome assembly for a R. riparia male generated using PacBio HiFi long-read sequencing and Hi-C scaffolding. The pseudohaploid assembly spans 1.19 Gb across 40 chromosome models and shows high completeness (97.6% BUSCO score). Repetitive elements make up 20.2% of the assembled chromosomes. A total of 19,624 protein-coding genes were annotated by integrating transcriptome evidence, ab initio gene prediction, and homology-based approaches. This high-quality reference genome provides a valuable foundation for studying population structure, adaptation, and evolutionary history in R. riparia. It serves as a critical resource for future assembly and investigation of the GRC, and contributes to a broader understanding of genome evolution in birds.