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BMC Genomics. 2018 Dec 20;19(1):952. doi: 10.1186/s12864-018-5355-9.

Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation.

Author information

1
Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
2
School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
3
Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA.
4
Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China.
5
Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, 266003, Shandong, China.
6
Department of Biology, University of Konstanz, 78464, Konstanz, Germany.
7
Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA. johnliu@syr.edu.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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.

KEYWORDS:

Adaptation; Air-breathing organ; Duplication; Evolution; Fish; Genome

PMID:
30572844
PMCID:
PMC6302426
DOI:
10.1186/s12864-018-5355-9
[Indexed for MEDLINE]
Free PMC Article

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