Transcriptomic sequencing reveals dynamic shifts in nutrient utilization and energy metabolism during embryonic and larval development of the purple sea urchin Heliocidaris crassispina
4 affiliations
- 1Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China AgricultuCral University, Guangzhou, 510642 People’s Republic of China
- 2State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 People’s Republic of China
- 3School of Medicine, Foshan University, Foshan, 528225 China
- 4Agro-Tech Extension Center of Guangdong Province, Huizhou, 516081 China
Abstract
Background: Heliocidaris crassispina is an economically important sea urchin in the Northwest Pacific, yet large-scale aquaculture is constrained by high mortality during early development. This limitation is largely attributable to the poor understanding of gene expression patterns across these critical stages. Therefore, a stage-resolved developmental transcriptomic profile from fertilization to the settled juvenile is needed to clarify the molecular basis of early developmental transitions and to support improved hatchery management and stage-appropriate feeding.
Results: We described a complete developmental profile of H. crassispina from fertilization to the settled juvenile and established transcriptomes for 14 consecutive developmental stages. Beginning with the two-arm pluteus stage, H. crassispina undergoes rapid growth, paralleling a marked rise in mortality that continues through metamorphosis until the juvenile settles. Based on global gene expression patterns, development was divided into four periods. Period-I spanned the fertilized egg to 32-cell stages, Period-II covered two late-cleavage stages (LC1–LC2), Period-III extended from blastula to two-arm pluteus, and Period-IV extended from the four-arm pluteus to the settled juvenile stages. GO and KEGG analyses indicated a stepwise transition in gene expression programs across developmental periods, consistent with the morphological and physiological changes observed. Weighted gene co-expression network analysis (WGCNA) identified ten modules whose expression profiles correlated significantly with specific developmental periods, indicating development is regulated by a coordinated, module-level transcriptional program. Analysis of digestive enzyme and energy metabolism genes showed that early embryos rely on endogenous reserves, whereas feeding larvae progressively establish exogenous digestive capacity, accompanied by stage-dependent fluctuations and a late-stage rise in glycolysis and TCA cycle gene expression, suggesting a metabolic transition associated with exogenous feeding and settlement.
Conclusion: This study established transcriptomes for 14 consecutive stages of H. crassispina from fertilization to the settled juvenile and, together with growth and survival, resolved four transcriptomic periods. Functional enrichment and WGCNA indicated coordinated, period-specific programs that track major morphological and physiological transitions. Digestive enzyme and energy metabolism genes showed a clear shift from reliance on endogenous reserves in embryos to the progressive establishment of exogenous digestive capacity in feeding larvae, accompanied by late-stage upregulation of glycolysis and TCA cycle genes around settlement. These insights support stage-specific feeding and hatchery management to reduce mortality.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12864-026-13190-z.
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BibTeX
@article{zhang2026transcriptomic,
title = {{Transcriptomic sequencing reveals dynamic shifts in nutrient utilization and energy metabolism during embryonic and larval development of the purple sea urchin Heliocidaris crassispina}},
author = {Zepeng Zhang and Fanjiang Ou and Jianfeng Xu and Zhou Qin and Wenjie Pan and Yi Zhang and Youkai Tu and Jiasheng Huang and Yang Liu and Aifen Yan and Haipeng Qin and Chunhua Ren and Chaoqun Hu and Hongyan Sun and Xiao Jiang and Ting Chen},
journal = {BMC Genomics},
year = {2026},
month = jul,
doi = {10.1186/s12864-026-13190-z},
url = {https://doi.org/10.1186/s12864-026-13190-z},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Transcriptomic sequencing reveals dynamic shifts in nutrient utilization and energy metabolism during embryonic and larval development of the purple sea urchin Heliocidaris crassispina
AU - Zepeng Zhang
AU - Fanjiang Ou
AU - Jianfeng Xu
AU - Zhou Qin
AU - Wenjie Pan
AU - Yi Zhang
AU - Youkai Tu
AU - Jiasheng Huang
AU - Yang Liu
AU - Aifen Yan
AU - Haipeng Qin
AU - Chunhua Ren
AU - Chaoqun Hu
AU - Hongyan Sun
AU - Xiao Jiang
AU - Ting Chen
PY - 2026
DA - 2026/07/30
JO - BMC Genomics
DO - 10.1186/s12864-026-13190-z
UR - https://doi.org/10.1186/s12864-026-13190-z
AB - Background: Heliocidaris crassispina is an economically important sea urchin in the Northwest Pacific, yet large-scale aquaculture is constrained by high mortality during early development. This limitation is largely attributable to the poor understanding of gene expression patterns across these critical stages. Therefore, a stage-resolved developmental transcriptomic profile from fertilization to the settled juvenile is needed to clarify the molecular basis of early developmental transitions and to support improved hatchery management and stage-appropriate feeding. Results: We described a complete developmental profile of H. crassispina from fertilization to the settled juvenile and established transcriptomes for 14 consecutive developmental stages. Beginning with the two-arm pluteus stage, H. crassispina undergoes rapid growth, paralleling a marked rise in mortality that continues through metamorphosis until the juvenile settles. Based on global gene expression patterns, development was divided into four periods. Period-I spanned the fertilized egg to 32-cell stages, Period-II covered two late-cleavage stages (LC1–LC2), Period-III extended from blastula to two-arm pluteus, and Period-IV extended from the four-arm pluteus to the settled juvenile stages. GO and KEGG analyses indicated a stepwise transition in gene expression programs across developmental periods, consistent with the morphological and physiological changes observed. Weighted gene co-expression network analysis (WGCNA) identified ten modules whose expression profiles correlated significantly with specific developmental periods, indicating development is regulated by a coordinated, module-level transcriptional program. Analysis of digestive enzyme and energy metabolism genes showed that early embryos rely on endogenous reserves, whereas feeding larvae progressively establish exogenous digestive capacity, accompanied by stage-dependent fluctuations and a late-stage rise in glycolysis and TCA cycle gene expression, suggesting a metabolic transition associated with exogenous feeding and settlement. Conclusion: This study established transcriptomes for 14 consecutive stages of H. crassispina from fertilization to the settled juvenile and, together with growth and survival, resolved four transcriptomic periods. Functional enrichment and WGCNA indicated coordinated, period-specific programs that track major morphological and physiological transitions. Digestive enzyme and energy metabolism genes showed a clear shift from reliance on endogenous reserves in embryos to the progressive establishment of exogenous digestive capacity in feeding larvae, accompanied by late-stage upregulation of glycolysis and TCA cycle genes around settlement. These insights support stage-specific feeding and hatchery management to reduce mortality. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12864-026-13190-z.
SN - 1471-2164
ER -