Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Develo
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ORIGINAL ARTICLE
Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Development and Function of the Bighead Catfish Clarias macrocephalus Xiaoli Ma 1,2 & Baofeng Su 1,2 & Max Bangs 1,2,3 & Veronica Alston 1,2 & Nathan J. C. Backenstose 1,2,4 & Rhoda Mae Simora 1,2,5 & Wenwen Wang 1,2 & De Xing 1,2 & Shangjia Li 1,2 & Zhi Ye 1,2,6 & Anthony G. Moss 2,7 & Thuy-Yen Duong 8 & Xu Wang 2,9,10 & Rex A. Dunham 1,2 Received: 23 June 2020 / Accepted: 18 October 2020 # Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air-breathing organ (ABO), while I. punctatus does 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 upon C. macrocephalus to compare with the non-air-breathing I. punctatus. Five-hundred million reads were generated and 25,239 expressed genes were annotated in C. macrocephalus. Among those, 8675 genes were differentially expressed across developmental stages. Comparative genomic analysis identified 1458 C. macrocephalus specific genes, which were absent in I. 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 in C. macrocephalus and offers insights into the adaption to hypoxic environments. Keywords Transcriptome analysis . Clarias macrocephalus . Air-breathing catfish . Oxygen binding . Oxygen transport
Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s10126-020-10005-4. * Xu Wang [email protected]
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College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao, 5023 Iloilo, Philippines
* Rex A. Dunham [email protected]
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Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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College of Aquaculture and Fisheries, Can Tho University, Can Tho City 94000, Vietnam
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School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
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Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
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Department of Biological Science, Florida State University, Tallahassee, FL 32304, USA
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Department of Pathobiology, Auburn University, Auburn, AL 36849, USA
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Department of Biological Sciences, Univer
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