National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China.
National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.
Int J Mol Sci. 2023 Aug 17;24(16):12892. doi: 10.3390/ijms241612892.
Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts.
沼虾科是具有两栖特征的硬骨鱼类谱系之一，生活在潮汐泥滩栖息地。与其他活跃的两栖鱼类不同，沼虾科物种通过生活在泥滩的深洞穴中，采取一种看似更为被动的生活方式，以规避与陆地生活相关的典型负面影响。然而，关于沼虾科在泥滩深洞适应方面的遗传起源知之甚少。在这里，我们对沼虾科的一个物种 sp. 进行了全基因组测序，以阐明其泥滩深洞适应的遗传基础。我们的结果显示，其组装基因组大小为 774.06Mb，包含 23 条假染色体，预测有 22399 个蛋白质编码基因。系统发育分析表明，sp. 大约在 28.3 百万年前与活跃的泥滩弹涂鱼分化开来。此外，在 sp. 中分别鉴定出 185 个和 977 个可能的基因家族发生扩张和收缩，有 172 个基因经历了正选择。显著扩张和选择的候选基因的富集类别主要与造血或血管生成、DNA 修复和免疫反应有关，这可能表明它们参与了对泥滩洞穴环境中常见的缺氧和多种病原体的适应。一些碳水化合物/脂质代谢和胰岛素信号相关基因也发生了显著改变，说明了与营养受限的地下环境相关的生理重塑。有趣的是，一些与视觉感知相关的基因（如晶体蛋白）明显缺失，表明它们在 sp. 小残余眼睛发育中的作用。我们的工作为理解沼虾科在泥滩深洞适应中的分子机制以及其他潮汐掘洞硬骨鱼类提供了有价值的资源。
