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

Li, Ning; Bao, Lisui; Zhou, Tao; Yuan, Zihao; Liu, Shikai; Dunham, Rex A.; Li, Yuanning; Wang, Kun; Xu, Xiaoyan; Jin, Yulin; Zeng, Qifan; Gao, Sen; Fu, Qiang; Liu, Yang; Yang, Yujia; Li, Qi; Meyer, Axel; Gao, Dongya; Liu, Zhanjiang

doi:10.1186/s12864-018-5355-9

Cited by 48 publications

(47 citation statements)

References 118 publications

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“…They have evolved an air‐breathing organ for respiring air not found in non‐air‐breathing fish. The analysis of the transcriptomes of gills versus the air‐breathing organ demonstrated the upregulation of hemoglobin and angiogenesis genes in the air‐breathing organ (Li et al, ). It is likely that this angiogenesis pathway is universal for all vertebrates and may function during some stages of fetal development.…”

Section: Circulatory System/rbcmentioning

confidence: 99%

The role of the red blood cell and platelet in the evolution of mammalian and avian endothermy

Soslau

2019

J Exp Zool Pt B

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This review presents evidence to support the hypothesis that the reduced O2 during the Permian/Triassic period was the impetus for the evolutionary selection of endothermic animals. The evolution of smaller red blood cells with greater surface areas along with increased: capillary density, capillary surface area, hematocrits, blood pressure, blood flow rates, and shear rates were critical for efficient gas exchange in endothermy. The evolution of the four‐chambered mammalian/avian heart allowed for low pulmonary and high systemic blood pressure. It is proposed that hypoxia‐induced angiogenesis led to increased vascularization in endothermic animals. The increased blood pressure, flow rates, and shear forces likely required changes in hemostatic mechanisms that were met in mammals by the evolution of anucleate platelets. The evolution of mammals and birds occurred in a parallel fashion with further genetic changes to anucleate RBCs/platelets occurring in mammals. Although it is possible that the evolution of endothermy in birds and mammals occurred as two independent events, it is more likely that a common ancestor developed genetic mutations that laid down the road map for parallel alterations of their cardiovascular system in response to environmental pressures. Model systems to support the proposed changes from ectotherm to endotherm were developed from published data. The evolutionary development of endothermy occurred over millions of years with a continuum of genetic alterations that involved skeletal, soft tissue, cardiovascular macrochanges along with numerous molecular alterations. Genetic signals and potential regulators for the evolutionary changes of endothermic blood cells from their bipotential stem cells are also proposed.

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Section: Circulatory System/rbcmentioning

confidence: 99%

The role of the red blood cell and platelet in the evolution of mammalian and avian endothermy

Soslau

2019

J Exp Zool Pt B

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“…Catfish also have an extremely sensitive sense of smell, particularly for amino acids. Furthermore, C. batrachus have significantly expanded olfactory gene families compared to nonamphibious catfishes, which may suggest a capacity for aerial olfaction (Li et al ., 2018).…”

Section: Discussionmentioning

confidence: 99%

“…Clariid catfishes also possess accessory air-breathing organs that include "fans" made of modified gill arches to ventilate air through this organ (Das, 1928;Liem, 1987). Some air-breathing fishes are known to use oxygen and carbon dioxide chemoreceptors in their gills to regulate aerial respiration (Hedrick & Jones, 1993;Lopes et al, 2010;Milsom, 2012 (Li et al, 2018).…”

Section: Batrachusmentioning

confidence: 99%

Why did the invasive walking catfish cross the road? Terrestrial chemoreception described for the first time in a fish

Bressman

Hill

Ashley‐Ross

2020

Journal of Fish Biology

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Clarias batrachus (walking catfish) is an invasive species in Florida, renowned for its air‐breathing and terrestrial locomotor capabilities. However, it is unknown how this species orients in terrestrial environments. Furthermore, while anecdotal life history information is widespread for this species in its nonnative range, little of this information exists in the literature. The goals of this study were to identify sensory modalities that C. batrachus use to orient on land, and to describe the natural history of this species in its nonnative range. Fish (n = 150) were collected from around Ruskin, FL, and housed in a greenhouse, where experiments took place. Individual catfish were placed in the center of a terrestrial arena and were exposed to nine treatments: two controls, L‐alanine, quinine, allyl isothiocynate, sucrose, volatile hydrogen sulphide, pond water and aluminium foil. These fish exhibited significantly positive chemotaxis toward alanine and pond water, and negative chemotaxis away from volatile hydrogen sulphide, suggesting chemoreception – both through direct contact and through the air – is important to their terrestrial orientation. Additionally, 88 people from Florida wildlife‐related Facebook groups who have personal observations of C. batrachus on land were interviewed for information regarding their terrestrial natural history. These data were combined with observations from 38 YouTube videos. C. batrachus appear to emerge most frequently during or just after heavy summer rains, particularly from stormwater drains in urban areas, where they may feed on terrestrial invertebrates. By better understanding the full life history of C. batrachus, we can improve management of this species.

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“…The protein sequences of channel catfish and tra catfish were obtained from the NCBI website to determine chromosome orthology ( Liu et al, 2016 ; Li et al, 2018 ; Zhou et al, 2018 ). The orthologs and orthogroups between channel catfish and tra catfish were identified using OrthoFinder version 2.2.7 ( Emms and Kelly, 2015 ).…”

Section: Methodsmentioning

confidence: 99%

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation

Shang

et al. 2021

Front. Genet.

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Tra catfish (Pangasianodon hypophthalmus), also known as striped catfish, is a facultative air-breather that uses its swim bladder as an air-breathing organ (ABO). A related species in the same order (Siluriformes), channel catfish (Ictalurus punctatus), does not possess an ABO and thus cannot breathe in the air. Tra and channel catfish serve as great comparative models for investigating possible genetic underpinnings of aquatic to land transitions, as well as for understanding genes that are crucial for the development of the swim bladder and the function of air-breathing in tra catfish. In this study, hypoxia challenge and microtomy experiments collectively revealed critical time points for the development of the air-breathing function and swim bladder in tra catfish. Seven developmental stages in tra catfish were selected for RNA-seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated, and a total of 21,448 unique genes were detected. A comparative genomic analysis between channel catfish and tra catfish revealed 76 genes that were present in tra catfish, but absent from channel catfish. In order to further narrow down the list of these candidate genes, gene expression analysis was performed for these tra catfish-specific genes. Fourteen genes were inferred to be important for air-breathing. Of these, HRG, GRP, and CX3CL1 were identified to be the most likely genes related to air-breathing ability in tra catfish. This study provides a foundational data resource for functional genomic studies in air-breathing function in tra catfish and sheds light on the adaptation of aquatic organisms to the terrestrial environment.

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

Cited by 48 publications

References 118 publications

The role of the red blood cell and platelet in the evolution of mammalian and avian endothermy

The role of the red blood cell and platelet in the evolution of mammalian and avian endothermy

Why did the invasive walking catfish cross the road? Terrestrial chemoreception described for the first time in a fish

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation

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