近日，浙江海洋大学韩志强及其课题组提出了大黄鱼的端粒到端粒基因组组装提供了对金黄色颜色进化的见解。相关论文于2025年9月18日发表在《遗传学报》杂志上。

研究小组构建了一个全长716.87 Mb、N50为31.75 Mb的端粒-端粒无间隙基因组组装（T2T-Larcro_1.0）。与目前的参考基因组（L_crocea_2.0）相比，T2T-Larcro_1.0包含112.70 Mb先前未组装的区域和2368个新锚定基因。该组合通过鉴定几种可能参与金黄色进化的候选基因（如OPNVA， nNOS, RDH13），促进了石首鱼的比较基因组学分析。转录组学分析进一步证实了OPNVA编码的脊椎动物古视蛋白（VA opsin）在大黄鱼皮肤组织中的表达，表明其作为视网膜外光感受器调节局部金黄色的作用。

整合基因组学和转录组学结果，他们的研究结果揭示了VA视蛋白的触发作用，将皮肤和神经光接受与L. crocea身体颜色变化（金黄色到银白色）的生理调节联系起来。总的来说，他们的发现提供了分子证据，阐明了藏红花金黄色的潜在进化机制。这种高质量的基因组组合也可以作为一种改良的生物进化、遗传改良和选择性育种的抗性。

据介绍，大黄鱼（Larimichthys crocea）是中国的旗舰海鱼，具有极高的商业价值和金黄色的颜色。然而，金黄色的遗传机制尚不清楚。

附：英文原文

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

Author: Zhiqiang Han a

Issue&Volume: 2025/09/18

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.

DOI: 10.1016/j.jgg.2025.09.006

Source: https://www.sciencedirect.com/science/article/abs/pii/S1673852725002462