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<p><i>Stichopus chloronotus</i> is a tropical sea cucumber with facultative asexual reproduction in the Indo-Western Pacific, yet its wild populations are decreasing due to extensive harvesting. Understanding the species’ genetic characteristics is essential for effective management and conservation. To develop novel microsatellite markers and assess the genetic diversity, clonality, and genetic structure of eight populations of <i>S. chloronotus</i> in the South China Sea, 193 individuals from eight populations across Wuzhizhou and Fenjiezhou (Boundary) islands were analyzed using nine newly developed microsatellite markers and five previously established markers. RNA-Seq was employed to obtained 62 662 unigenes and identified 16 926 microsatellite loci. Fourteen polymorphic microsatellite loci were developed, of which 11 were highly polymorphic (polymorphic information content&gt;0.5). The number of alleles (<i>N</i><sub>a</sub>) ranged from 3 to 6 per locus, and the average Shannon diversity index (<i>I</i>) was 1.107. All the populations exhibited asexual reproduction, with regional variations in reproductive modes. Asexual reproduction was predominant in the northwestern Wuzhizhou Island population (SY 7) and the Fenjiezhou Island population (LS 8), where four and five predominant clones represented more than 89% of the individuals, which led to reduced genetic diversity. Overall, genetic diversity was moderately low, with significant genetic differentiation among populations (<i>F</i><sub>ST</sub>=0.33; <i>P</i>&lt;0.001), suggesting limited gene flow (the number of migrants (<i>N</i><sub>m</sub>) &lt;1). These findings highlight the role of reproductive strategies in shaping fine-scale genetic differentiation in <i>S. chloronotus</i>. The limited recruitment success of sexually produced larvae and habitat heterogeneity likely constrain clone dispersal, contributing to distinct genetic restructuring. This study provided key insights into the interplay between reproductive strategies and genetic patterns in sea cucumbers, offering a scientific basis for targeted conservation efforts.</p>

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Using novel microsatellite markers to characterize genetics of asexual sea cucumber Stichopus chloronotus populations in tropical nearshore islands of the South China Sea

  • 期刊论文

  • 发表日期：

    2025年10月4日

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  • Xiang Hu,
  • Xinxin Huang,
  • Mengjiao Liu,
  • Linwen He,
  • Fei Gao,
  • Qiang Xu

摘要

Stichopus chloronotus is a tropical sea cucumber with facultative asexual reproduction in the Indo-Western Pacific, yet its wild populations are decreasing due to extensive harvesting. Understanding the species’ genetic characteristics is essential for effective management and conservation. To develop novel microsatellite markers and assess the genetic diversity, clonality, and genetic structure of eight populations of S. chloronotus in the South China Sea, 193 individuals from eight populations across Wuzhizhou and Fenjiezhou (Boundary) islands were analyzed using nine newly developed microsatellite markers and five previously established markers. RNA-Seq was employed to obtained 62 662 unigenes and identified 16 926 microsatellite loci. Fourteen polymorphic microsatellite loci were developed, of which 11 were highly polymorphic (polymorphic information content>0.5). The number of alleles (Na) ranged from 3 to 6 per locus, and the average Shannon diversity index (I) was 1.107. All the populations exhibited asexual reproduction, with regional variations in reproductive modes. Asexual reproduction was predominant in the northwestern Wuzhizhou Island population (SY 7) and the Fenjiezhou Island population (LS 8), where four and five predominant clones represented more than 89% of the individuals, which led to reduced genetic diversity. Overall, genetic diversity was moderately low, with significant genetic differentiation among populations (FST=0.33; P<0.001), suggesting limited gene flow (the number of migrants (Nm) <1). These findings highlight the role of reproductive strategies in shaping fine-scale genetic differentiation in S. chloronotus. The limited recruitment success of sexually produced larvae and habitat heterogeneity likely constrain clone dispersal, contributing to distinct genetic restructuring. This study provided key insights into the interplay between reproductive strategies and genetic patterns in sea cucumbers, offering a scientific basis for targeted conservation efforts.