Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby Taenioides sp. (Teleost: Amblyopinae).
Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby Taenioides sp. (Teleost: Amblyopinae).
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DOI：
10.3390/ijms241612892
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发表时间：
2023-08-17
影响因子：
5.6
通讯作者：
Liu, Liqin
中科院分区：
文献类型：
--
作者：
Liu, Yantao;Liu, Tianwei;Wang, Yuzhen;Liu, Jing;Liu, Bingjian;Gong, Li;Lu, Zhenming;Liu, Liqin
钝眼鲷亚科是生活在潮滩生境中的硬骨鱼的一个谱系，保留了两栖特征。与其他活跃的两栖鱼类相比，钝眼鱼亚科的物种采取了更为被动的生活方式，生活在泥滩的深洞中，以规避与陆地相关的典型负面影响。然而，很少有人知道这些泥滩深挖洞适应Amblyopinae的遗传起源。在这里，我们测序了第一个Amblyopinae物种的基因组，Taenioides sp.，以阐明它们在泥滩的深穴适应。我们的结果显示，组装的基因组大小为774.06 Mb，锚定了23条假染色体，预测了22，399个蛋白质编码基因。系统发育分析表明，带形鱼（Taenioides sp.）与弹涂鱼（Mudskipper）的亲缘关系约为28.3Ma。另外，在带绦虫属中分别鉴定出185个和977个基因家族处于扩增、收缩状态，172个基因经历了正选择，分别在显著扩增和选择下的顶级候选基因的富集类别主要与造血或血管生成、DNA修复和免疫反应相关，这可能表明它们参与了对通常在泥滩穴居环境中观察到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基因也显着改变，说明与营养有限的地下环境相关的生理重塑。有趣的是，与视觉感知相关的几个基因（例如，晶体蛋白）经历了明显的基因丢失，指出他们的作用，在小退化的眼睛发育带属。我们的工作提供了宝贵的资源，了解分子机制的泥滩深挖洞适应Amblyopinae，以及在其他潮汐穴居硬骨鱼。
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, Taenioides 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 Taenioides 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 Taenioides 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 Taenioides 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.
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影响因子：
48
作者：
Cheng H;Concepcion GT;Feng X;Zhang H;Li H
通讯作者：
Li H
影响因子：
8.8
作者：
Fang X;Seim I;Huang Z;Gerashchenko MV;Xiong Z;Turanov AA;Zhu Y;Lobanov AV;Fan D;Yim SH;Yao X;Ma S;Yang L;Lee SG;Kim EB;Bronson RT;Šumbera R;Buffenstein R;Zhou X;Krogh A;Park TJ;Zhang G;Wang J;Gladyshev VN
通讯作者：
Gladyshev VN
影响因子：
9.3
作者：
Durand NC;Shamim MS;Machol I;Rao SS;Huntley MH;Lander ES;Aiden EL
通讯作者：
Aiden EL
影响因子：
14.9
作者：
Keilwagen J;Wenk M;Erickson JL;Schattat MH;Grau J;Hartung F
通讯作者：
Hartung F
影响因子：
3.4
作者：
Farnsworth DR;Posner M;Miller AC
通讯作者：
Miller AC