Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
BMC Genomics. 2018 Dec 20;19(1):952. doi: 10.1186/s12864-018-5355-9.
Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes "walks" to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life.
Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1-2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish.
This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life.
攀鲈（Clarias batrachus）是一种能够在空气中呼吸并在陆地上移动的淡水鱼。它通常栖息在各种低氧栖息地中，在泥滩中挖洞，有时在夏季会“行走”以寻找合适的环境。它已经进化出辅助呼吸器官来呼吸空气，并具有相应的机制来在这种具有挑战性的环境中生存。因此，它是研究适应陆地生活的理想模型。
与斑点叉尾鮰（Ictalurus punctatus）进行比较基因组学研究揭示了攀鲈在 DNA 修复、酶激活剂活性和小 GTP 酶调节活性方面的特定适应性。与 11 种非空气呼吸鱼类的比较分析表明，基因表达和含氮废物代谢过程发生了适应性进化。此外，在空气呼吸的攀鲈基因组中发现肌红蛋白、与 A 类 G 蛋白偶联受体 1 相关的嗅觉受体和磺基转移酶 6b1 基因发生了扩张，分别有 15、15 和 12 个拷贝，而不具备这些基因 1-2 个拷贝的非空气呼吸鱼类。此外，我们还测序并比较了鳃和空气呼吸器官的转录组，以表征涉及弹性纤维形成、氧气结合和运输、血管生成、离子稳态和酸碱平衡的空气呼吸机制。血红蛋白基因在攀鲈的空气呼吸器官中的表达显著高于鳃。
本研究为了解攀鲈适应陆地环境的机制提供了重要的基因组资源。通过肌红蛋白基因的基因组扩张和血红蛋白及血管生成相关基因的转录组上调来增强氧气储存和运输能力，可能是这种水生物种适应陆地生活的分子基础的重要组成部分。
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