A telomere-to-telomere genome assembly of the large yellow croaker provides insights into evolution of golden-yellow coloration

Shengyong Xu; Qi Liu; Tianyan Yang; Zhiqiang Han

doi:10.1016/j.jgg.2025.09.006

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A telomere-to-telomere genome assembly of the large yellow croaker provides insights into evolution of golden-yellow coloration

doi: 10.1016/j.jgg.2025.09.006

a. Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China;
b. College of Fisheries, Southwest University, Chongqing 400715, China

Funds:

This work was supported by the National Key Research and Development Program of China (2023YFD2401901) and the Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes (2024J004).

Received Date: 2025-08-10
Accepted Date: 2025-09-13
Rev Recd Date: 2025-09-12

Available Online: 2025-09-19

Abstract

Abstract

The large yellow croaker (Larimichthys crocea) is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration. However, the genetic mechanisms underlying golden-yellow coloration remain unclear. Here, we construct a telomere-to-telomere gap-free genome assembly (T2T-Larcro_1.0) spanning 716.87 Mb, with a contig N50 of 31.75 Mb. Compared to the current reference genome (L_crocea_2.0), T2T-Larcro_1.0 incorporates 112.70 Mb of previously unassembled regions and 2368 newly anchored genes. This assembly facilitates comparative genomics analyses in sciaenids by identifying several candidate genes (e.g., OPNVA, nNOS, RDH13) potentially involved in evolution of golden-yellow coloration. Transcriptomic analyses further confirm expression of OPNVA-encoded vertebrate ancient opsin (VA opsin) in skin tissues of the large yellow croaker, suggesting its role as an extraretinal photoreceptor regulating localized golden-yellow coloration. Integrating genomics and transcriptomics results, our results uncover the triggering effect of VA opsin linking skin and neural photoreception to physiological regulation of body color change (golden-yellow to silvery-white) in L. crocea. Collectively, our findings provide molecular evidence that elucidate the underlying evolutionary mechanism of golden-yellow coloration in L. crocea. This high-quality genome assembly also serves as an improved resource for biological evolution, genetic improvement, and selective breeding of L. crocea.
- T2T genome assembly,
- Vertebrate ancient opsin,
- Body coloration,
- Extraretinal photoreception,
- Sciaenidae

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