Yan Yujie, Seim Inge, Guo Yang, Chi Xupeng, Zhong Zhaoshan, Wang Dantong, Li Mengna, Wang Haining, Zhang Huan, Wang Minxiao, Li Chaolun
CAS Key Laboratory of Marine Ecology and Environmental Sciences, and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Biol. 2025 Jan 13;23(1):13. doi: 10.1186/s12915-025-02112-2.
Lindaspio polybranchiata, a member of the Spionidae family, has been reported at the Lingshui Cold Seep, where it formed a dense population around this nascent methane vent. We sequenced and assembled the genome of L. polybranchiata and performed comparative genomic analyses to investigate the genetic basis of adaptation to the deep sea. Supporting this, transcriptomic and fatty acid data further corroborate our findings.
We report the first genome of a deep-sea spionid, L. polybranchiata. Over long-term adaptive evolution, genes associated with vision and biological rhythmicity were lost, which may indirectly benefit oligotrophy by eliminating energetically costly processes. Compared to its shallow-sea relatives, L. polybranchiata has a significantly higher proportion of polyunsaturated fatty acids (PUFAs) and expanded gene families involved in the biosynthesis of unsaturated fatty acids and chromatin stabilization, possibly in response to high hydrostatic pressure. Additionally, L. polybranchiata has broad digestive scope, allowing it to fully utilize the limited food resources in the deep sea to sustain a large population. As a pioneer species, L. polybranchiata has an expanded repertoire of genes encoding potential chemoreceptor proteins, including ionotropic receptors (IRs) and gustatory receptor-like receptors (GRLs). These proteins, characterized by their conserved 3D structures, may enhance the organism's ability to detect chemical cues in chemosynthetic ecosystems, facilitating rapid settlement in suitable environments.
Our results shed light on the adaptation of Lindaspio to the darkness, high hydrostatic pressure, and food deprivation in the deep sea, providing insights into the molecular basis for L. polybranchiata becoming a pioneer species.
多鳃内卷齿蚕是蛰龙介科的一员，在陵水冷泉被发现，它在这个新形成的甲烷喷口周围形成了密集的种群。我们对多鳃内卷齿蚕的基因组进行了测序和组装，并进行了比较基因组分析，以研究其适应深海的遗传基础。转录组学和脂肪酸数据进一步证实了我们的发现。
我们报道了首个深海蛰龙介科物种——多鳃内卷齿蚕的基因组。在长期的适应性进化过程中，与视觉和生物节律相关的基因丢失了，这可能通过消除高耗能过程间接地有利于寡营养状态。与浅海近亲相比，多鳃内卷齿蚕具有显著更高比例的多不饱和脂肪酸（PUFA），以及参与不饱和脂肪酸生物合成和染色质稳定的基因家族扩张，这可能是对高静水压力的响应。此外，多鳃内卷齿蚕具有广泛的消化范围，使其能够充分利用深海中有限的食物资源来维持大量种群。作为先锋物种，多鳃内卷齿蚕拥有扩展的编码潜在化学感受器蛋白的基因库，包括离子型受体（IR）和味觉受体样受体（GRL）。这些具有保守三维结构的蛋白质可能增强生物体在化学合成生态系统中检测化学信号的能力，便于在适宜环境中快速定居。
我们的研究结果揭示了多鳃内卷齿蚕对深海黑暗、高静水压力和食物匮乏的适应性，为多鳃内卷齿蚕成为先锋物种的分子基础提供了见解。
