Uncovering a sex determination region and female specific markers in the Crown-of-thorns starfish

Yanlin Wang; Xiao Du; Scott Cummins; Wei Wang; Xiaoxu Li; Gang Ni; Muyan Chen

doi:10.21203/rs.3.rs-9754053/v1

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Uncovering a sex determination region and female specific markers in the Crown-of-thorns starfish

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Uncovering a sex determination region and female specific markers in the Crown-of-thorns starfish

Yanlin Wang, Xiao Du, Scott Cummins, Wei Wang, Xiaoxu Li, Gang Ni and Muyan Chen

Research Square , Vol.16 June 2026

Research Square Company

2026

DOI: https://doi.org/10.21203/rs.3.rs-9754053/v1

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Abstract

Sex determination

Crown-of-thorns starfish

Sex molecular marker

Whole-genome resequencing

Population outbreaks of Crown-of-thorns starfish (COTS) in the Indo-Pacific region have inflicted devastating damage on coral reef ecosystems. Manual culling remains the most effective control method against this marine pest, but it entails substantial labor and economic costs. Emerging research focused on the COTS biology, including molecular biology, has provided foundational insights that may support the development of new approaches to mitigate future population outbreaks. However, limited understanding of its sex determination mechanism and the absence of non-invasive sex identification methods have impeded sex-related research and the development of effective biocontrol strategies. Therefore, we performed high-coverage whole-genome re-sequencing of 30 COTS females and 30 COTS males to identify candidate sex determination regions, and developed sex-specific molecular markers. The distribution of sex-associated SNPs and sex-specific SNPs, along with the selection signatures of fixation index indicated that a 11–14 Mb physical region within COTS chromosome 10 was a candidate sex determination region. Within this region, the PKNOX2 gene, harboring numerous sex-associated SNPs and showing testis-biased expression, might influence sexual dimorphism. We successfully developed two pairs of female-specific molecular markers, which were validated in separate populations with 100% accuracy, enabling the non-invasive identification of the genetic sex in COTS. In addition, the identification of female-specific sequences and the genotypes of sex-specific SNPs suggested COTS might possess a ZZ/ZW sex determination system. Our study not only provides novel insights into the diverse sex determination mechanisms in echinoderms, but also establishes a genetic foundation for sex-related physiological research and the future development of biocontrol strategies against COTS.

Details

Title: Uncovering a sex determination region and female specific markers in the Crown-of-thorns starfish
Authors: Yanlin Wang (Author) - Ocean University of China
Xiao Du - BGI Research
Scott Cummins - University of the Sunshine Coast
Wei Wang (Author) - Third Institute of Oceanography
Xiaoxu Li - Hainan University
Gang Ni (Author) - Ocean University of China
Muyan Chen (Corresponding Author) - Ocean University of China
Publication details: Research Square , Vol.16 June 2026
Publisher: Research Square Company
Date published: 2026
DOI: 10.21203/rs.3.rs-9754053/v1
Copyright note: This work is licensed under a Creative Commons Attribution 4.0 International License.
Data Availability: The whole-genome re-sequencing data have been deposited in the Genome Sequence Archive (GSA, accession number: CRA042951), which are publicly accessible through BioProject PRJCA064069 (https://ngdc.cncb.ac.cn/).
Grant note: National Key Research and Development Program, China [2022YFC3106301] and Natural Science Foundation of Shandong Province [No. ZR2025MS589].
Organisation Unit: Centre for Bioinnovation
Language: English
Record Identifier: 991252399302621
Output Type: Preprint

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