Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Development and Function of the Bighead Catfish Clarias macrocephalus

Ma, Xiaoli; Su, Baofeng; Bangs, Max R.; Alston, Veronica; Backenstose, Nathan J. C.; Simora, Rhoda Mae C.; Wang, Wenwen; Xing, De; Li, Shangjia; Liu, Yang; Moss, Anthony G.; Yên, Dương Thúy; Wang, Xu; Dunham, Rex A.

doi:10.1007/s10126-020-10005-4

Cited by 7 publications

(5 citation statements)

References 43 publications

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“…HIF-1 was found important for hypoxia in red swamp cray fish ( Xu et al, 2022 ). With bighead catfish, Ma et al (2021) identified 26 candidate genes involved in air-breathing development and function.…”

Section: Review Of Recent Progress Of Genetic and Epigenetic Studies ...mentioning

confidence: 99%

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

2022

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Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.

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Section: Review Of Recent Progress Of Genetic and Epigenetic Studies ...mentioning

confidence: 99%

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

2022

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“…Nuclear genome sequences. To date, complete genome sequence studies have been carried out for C. batrachus (Li et al, 2018), C. magur (Kushwaha et al, 2021), and C. macrocephalas (Duong et al, 2020;Ma et al, 2021)). The work on C. batrachus from Li et al (2018) provided an estimate of the total genome size (~821 Mb), the estimated number of genes (22,914), and the percent of repetitive DNA sequences found in this species (30.3%).…”

Section: Genome Level Characterizationsmentioning

confidence: 99%

“…For C. macrocephalus, the work of Duong et al (2020) generated a dataset indicating a larger total genome size (883 Mb) and an intermediate number of annotated genes (21,124). The work of Ma et al (2021) on this same species will be discussed in more detail below.…”

Section: Genome Level Characterizationsmentioning

confidence: 99%

“…In work on C. macrocephalus, Duong et al (2020) described two genes, mb (as described above) and an olfactory receptor gene (ora1), as being associated with adaptations to air-breathing ability and a semi-terrestrial lifestyle. Ma et al (2021) reported on a study of both the C. macrocephalus genome and transcriptome to identify a gene in this air-breathing catfish that were either not present or…”

Section: Genome Level Characterizationsmentioning

confidence: 99%

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Biology of selected Clarias catfish species used in aquaculture

Haymer

Khedkar

2022

Israeli Journal of Aquaculture - Bamidgeh

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Catfish are important organisms used extensively in aquaculture. For this review, we are focusing on specific species of catfish in the genus Clarias, primarily Clarias batrachus, C. gariepinus and C. macrocephalus, because of their widespread use in aquaculture and the considerable amount of information that has been amassed on different aspects of their biology. This review summarizes information available on topics ranging from the taxonomy and geographic distribution of these catfish to work done on them at the genetic, molecular biological and genomic levels. This information may be useful in future efforts to grow and expand their use in aquaculture.

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“…Since fish air-breathing is an important evolutionary adaptation for aquatic hypoxia, it has fascinated researchers for at least a century [ 1 , 2 , 3 ]. Up to now, about 400 species of fish have been reported to have the ability of assisted air-breathing [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Fibronectin 1B Gene Plays an Important Role in Loach Barbel Air-Breathing

Sun

Huang

et al. 2021

IJMS

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Loach (Misgurnus anguillicaudatus) is well known to perform air-breathing through the posterior intestine and skin. However, we find here for the first time a unique central vascular structure in the loach barbel, with a blood–gas diffusion distance as short as that of the posterior intestine. Under acute hypoxia, the distance of loach barbels became significantly shorter. Moreover, barbel removal significantly decreased air-breathing frequency of the loach. These findings imply that the barbel is another air-breathing organ of the loach. For further investigation of loach barbel air-breathing, a transcriptome analysis of barbels with air exposure treatment was performed. A total of 2546 differentially expressed genes (DEGs) between the T-XU (air exposure) and C-XU (control) group were identified, and 13 key DEGs related to barbel air-breathing were screened out. On this foundation, sequence, expression, and location analysis results indicated an important positive role of fibronectin 1b (fn1b) in loach barbel air-breathing. We further generated an fn1b-depletion loach (MT for short) using the CRISPR/Cas9 technique. It was indicated that depletion of fn1b could weaker barbel air-breathing ability. In conclusion, due to nonlethal and regenerative characteristics, the loach barbel, a newly discovered and fn1b-related fish air-breathing organ, can be a good model for fish air-breathing research.

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Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Development and Function of the Bighead Catfish Clarias macrocephalus

Cited by 7 publications

References 43 publications

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Biology of selected Clarias catfish species used in aquaculture

Fibronectin 1B Gene Plays an Important Role in Loach Barbel Air-Breathing

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