Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Development and Function of the Bighead Catfish Clarias macrocephalus
Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Development and Function of the Bighead Catfish Clarias macrocephalus
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比较基因组和转录组分析揭示了与鳙鱼呼吸空气发育和功能有关的 26 个候选基因
DOI：
10.1007/s10126-020-10005-4
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发表时间：
2021
影响因子：
3
通讯作者：
Ye, Zhi
中科院分区：
文献类型：
--
作者：
Ma, Xiaoli;Su, Baofeng;Bangs, Max;Alston, Veronica;Backenstose, Nathan J.;Simora, Rhoda Mae;Wang, Wenwen;Xing, De;Li, Shangjia;Ye, Zhi
大头鲶（Clarias macrocephalus）和癍点叉尾（Ictalurus punctatus）是鲇形目的淡水鱼类。macrocephalus既有鳃，也有作为呼吸器官（ABO）的改良鳃结构，而I. punctatus没有这样的器官，不能在空气中呼吸，为研究硬骨鱼ABO发育的分子基础提供了一个很好的模型。为了研究空气呼吸功能发育的关键时间窗，基于缺氧激发结果选择了七个发育阶段，并在C.大头症与非空气呼吸I.斑点状。产生了五亿个读段，并在C中注释了25，239个表达的基因。大头畸形其中，8675个基因在不同发育阶段差异表达。比较基因组分析鉴定了1458 C。macrocephalusspecific gene，I.斑点状。基因网络和蛋白质-蛋白质相互作用分析确定了26个参与呼吸功能的关键基因。mb、ngb、hexamethasone三个最重要的候选基因主要与携氧、氧结合和血红素结合活性相关。我们的研究为探索呼吸功能的基因组基础提供了丰富的数据。macrocephalusand提供了对低氧环境适应的见解。
The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order.C. macrocephalushas both gills and modified gill structures serving as an air-breathing organ (ABO), whileI. punctatusdoes not possess such an organ, and cannot breathe in air, providing an excellent model for studying the molecular basis of ABO development in teleost fish. To investigate the critical time window for the development of air-breathing function, seven development stages were selected based on hypoxia challenge results, and RNA-seq was performed uponC. macrocephalusto compare with the non-air-breathingI. punctatus. Five-hundred million reads were generated and 25,239 expressed genes were annotated inC. macrocephalus. Among those, 8675 genes were differentially expressed across developmental stages. Comparative genomic analysis identified 1458C. macrocephalusspecific genes, which were absent inI. punctatus. Gene network and protein-protein interaction analyses identified 26 key hub genes involved in the air-breathing function. Three top candidate genes,mb,ngb,hbae, are mainly associated with oxygen carrying, oxygen binding, and heme binding activities. Our study provides a rich data set for exploring the genomic basis of air-breathing function inC. macrocephalusand offers insights into the adaption to hypoxic environments.
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