Using novel microsatellite markers to characterize genetics of asexual sea cucumber <italic style="font-style: italic">Stichopus</italic> <italic style="font-style: italic">chloronotus</italic> populations in tropical nearshore islands of the South China Sea

Xiang HU; Xinxin HUANG; Mengjiao LIU; Linwen HE; Fei GAO; Qiang XU

doi:10.1007/s00343-025-4339-2

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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

Ecology | Updated：2026-03-26

- Using novel microsatellite markers to characterize genetics of asexual sea cucumber Stichopus chloronotus populations in tropical nearshore islands of the South China Sea
- Journal of Oceanology and Limnology Vol. 44, Issue 1, Pages: 219-233(2026)
- Affiliations：
  
  1.State Key Laboratory of Marine Resource Utilization in South China Sea, Haikou 570228, China
  2.College of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
  3.School of Ecology, Hainan University, Haikou 570228, China
- Author bio：
  
  xuqianghnu@hainanu.edu.cn
- Funds：
- DOI：10.1007/s00343-025-4339-2
  CLC：
- Received：11 December 2024，
  
  Accepted：11 February 2025，
  
  Online First：18 March 2025，
  
  Published：01 January 2026
- Accepted：
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HU Xiang,HUANG Xinxin,LIU Mengjiao,et al.Using novel microsatellite markers to characterize genetics of asexual sea cucumber Stichopus chloronotus populations in tropical nearshore islands of the South China Sea[J].Journal of Oceanology and Limnology,2026,44(01):219-233.
DOI：

HU Xiang,HUANG Xinxin,LIU Mengjiao,et al.Using novel microsatellite markers to characterize genetics of asexual sea cucumber Stichopus chloronotus populations in tropical nearshore islands of the South China Sea[J].Journal of Oceanology and Limnology,2026,44(01):219-233. DOI： 10.1007/s00343-025-4339-2.

摘要

Abstract

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

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 (

) ranged from 3 to 6 per locus

and the average Shannon diversity index (

) was 1.107. All the populations exhibited asexual reproduction

with regional variations in reproductive mode

s. 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 (

=0.33;

0.001)

suggesting limited gene flow (the number of migrants (

)

1). These findings highlight the role of reproductive strategies in shaping fine-scale genetic differentiation in

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.

关键词

Keywords

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DOI：10.1007/s00343-025-4339-2

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