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Abstract <p>Avian genomes are remarkably conserved in size, though subtle interspecific differences may reflect evolutionary adaptations. We employed k-mer analysis to estimate genome sizes of two galliform species <i>Alectoris chukar</i> and <i>Francolinus francolinus</i> using whole-genome sequencing data processed via Meryl on the Galaxy platform. Our results revealed that <i>Francolinus francolinus</i> has a consistently larger genome (1.16–1.17 Gb) than <i>Alectoris chukar</i> (1.13–1.15 Gb). The minimal variation (&lt;2%) between estimates from 19-mer and 21-mer analyses supports the robustness of this computational method. Both datasets were sequenced at depths exceeding 40× and 100×, respectively, well above the recommended 25× threshold for reliable genome size estimation. This study establishes the first genome size estimates for these species through k-mer frequency analysis, demonstrating that k-mer-based quantification serves as a robust and reliable alternative to conventional cytometric methods for genome size determination. These findings establish a genomic baseline for future comparative studies of Galliformes and demonstrate the utility of short-read sequencing combined with k-mer analysis in avian genomics.</p>

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K-mer-Based Genome Size Estimation in Alectoris chukar and Francolinus francolinus: Insights from Whole-Genome Sequencing

  • 期刊论文

  • 发表日期：

    2026年2月1日

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  • P. Yousif,
  • A. A. Abdi,
  • S. I. Mustafa

摘要

Abstract

Avian genomes are remarkably conserved in size, though subtle interspecific differences may reflect evolutionary adaptations. We employed k-mer analysis to estimate genome sizes of two galliform species Alectoris chukar and Francolinus francolinus using whole-genome sequencing data processed via Meryl on the Galaxy platform. Our results revealed that Francolinus francolinus has a consistently larger genome (1.16–1.17 Gb) than Alectoris chukar (1.13–1.15 Gb). The minimal variation (<2%) between estimates from 19-mer and 21-mer analyses supports the robustness of this computational method. Both datasets were sequenced at depths exceeding 40× and 100×, respectively, well above the recommended 25× threshold for reliable genome size estimation. This study establishes the first genome size estimates for these species through k-mer frequency analysis, demonstrating that k-mer-based quantification serves as a robust and reliable alternative to conventional cytometric methods for genome size determination. These findings establish a genomic baseline for future comparative studies of Galliformes and demonstrate the utility of short-read sequencing combined with k-mer analysis in avian genomics.