International Journal of Molecular Zoology 2025, Vol.15, No.2 http://animalscipublisher.com/index.php/ijmz © 2025 AnimalSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
International Journal of Molecular Zoology 2025, Vol.15, No.2 http://animalscipublisher.com/index.php/ijmz © 2025 AnimalSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Publisher AnimalSci Publisher Editedby Editorial Team of International Journal of Molecular Zoology Email: edit@ijmz.animalscipublisher.com Website: http://animalscipublisher.com/index.php/ijmz Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada International Journal of Molecular Zoology (ISSN 1927-534X) is an open access, peer reviewed journal published online by AnimalSci Publisher. The journal is publishing all the latest and outstanding research articles, letters and reviews in all aspects of molecular zoology, containing behavior, structure, evolution, classification, habits and distribution of animals, also including the relative fields on embryology, developmental biology, systematics, genetics and genomics, ecology, physiology, as well as biochemistry. Meanwhile we also publish the articles related to basic research, such as anatomy, morphology and taxonomy, which are fundamental to molecular technique’s innovation and development. AnimalSci Publisher is an international Open Access publisher specializing in animal molecular breeding, including molecular zoology and relative fields registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. All the articles published in International Journal of Molecular Zoology are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. AnimalSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
International Journal of Molecular Zoology (online), 2025, Vol. 15, No.2 ISSN 1927-534X http://animalscipublisher.com/index.php/ijmz © 2025 AnimalSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Genomic Basis and Evolutionary Adaptation Mechanisms of Hypoxia Tolerance in Catfish Baohua Dong, Xianming Li International Journal of Molecular Zoology, 2025, Vol. 15, No. 2, 48-57 The Evolutionary Genomics of Giant African Land Snail (Lissachatina fulica): Insights from Whole-Genome Sequencing and Structural Variations Wei Liu, Jia Chen International Journal of Molecular Zoology, 2025, Vol. 15, No. 2, 58-68 Origin Domestication and Global Expansion of Domestic Geese Jun Li, Xiaoli Chen International Journal of Molecular Zoology, 2025, Vol. 15, No. 2, 69-77 Global Distribution Patterns of Snakes, Their Historical Climatic Drivers Hongbo Liang, Qibin Xu International Journal of Molecular Zoology, 2025, Vol. 15, No. 2, 78-89 Hybridization Strategies to Improve Growth Rate and Egg Production in Chickens Jun Wang, Shiqiang Huang International Journal of Molecular Zoology, 2025, Vol. 15, No. 2, 90-100
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 48 Research Insight Open Access Genomic Basis and Evolutionary Adaptation Mechanisms of Hypoxia Tolerance inCatfish Baohua Dong1, Xianming Li 2 1 Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China 2 Aquatic Biology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding author: xianming.li@cuixi.org International Journal of Molecular Zoology, 2025, Vol.15, No.2 doi: 10.5376/ijmz.2025.15.0006 Received: 10 Jan., 2025 Accepted: 15 Feb., 2025 Published: 12 Mar., 2025 Copyright © 2025 Dong and Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Dong B.H., and Li X.M., 2025, Genomic basis and evolutionary adaptation mechanisms of hypoxia tolerance in catfish, International Journal of Molecular Zoology, 15(2): 48-57 (doi: 10.5376/ijmz.2025.15.0006) Abstract This study analyzes the physiological adaptation characteristics, genomic basis, and evolutionary mechanisms of catfish hypoxia tolerance, and summarizes the recent research progress in functional genomics. The study finds that catfish show unique behavioral adjustments (such as reduced activity and surface breathing) and respiratory system modifications under hypoxic conditions, and adapt to oxygen deficiency by reducing metabolic rate and strengthening anaerobic metabolism. At the genomic level, catfish hypoxia tolerance involves the expansion or regulatory optimization of core hypoxia signaling pathway genes such as HIF, the adaptation of energy metabolism-related genes, the efficient mobilization of antioxidant and stress response genes, and evolutionary changes in the hemoglobin gene family. This paper also lists typical examples of hypoxia tolerance evolution in catfish species, such as channel catfish and other related species, and discusses the prospects of applying hypoxia-tolerant genetic traits to aquaculture breeding, as well as strategies to enhance the resilience of freshwater fisheries in the context of climate change. This study deepens the understanding of the genomic basis and evolutionary mechanisms of catfish hypoxia tolerance, which is of great significance for aquaculture strain improvement and research on fish adaptive evolution. Keywords Catfish; Hypoxia tolerance; HIF pathway; Genomic adaptation; Evolutionary mechanism; Aquaculture breeding 1 Introduction In recent decades, due to factors such as climate warming and eutrophication, the hypoxic areas of water bodies around the world (dissolved oxygen below 2 mg/L) have expanded significantly. Hypoxia is considered to be an important stressor affecting aquatic ecosystems, which can have adverse effects on the behavior, development, survival and reproduction of fish (Murphy and Rees, 2024). When the dissolved oxygen content in water drops below the threshold, many fish show phenomena such as decreased swimming ability, reduced feeding, restricted habitats and even large-scale deaths. For example, hypoxic "dead zones" in oceans and freshwaters have posed a serious threat to fishery resources (Diaz and Rosenberg, 2008; Bailey et al., 2020). Faced with hypoxic stress, different fish have evolved a variety of tolerance strategies, including behavioral avoidance or respiratory adjustments, physiological changes in ventilation and circulatory systems, and biochemical metabolic reprogramming. Studying the hypoxic adaptation mechanism of fish is not only of great significance to ecology, but also provides a scientific basis for aquaculture to cope with environmental changes (Wang et al., 2023). Catfishes in the Siluriformes family are known for their high ecological diversity and tolerance to harsh environments. Many of these species inhabit warm, slow-flowing, and even severely hypoxic waters, such as swamps, rice fields, and mud ponds. The ecological success of catfishes is largely due to their outstanding tolerance to low oxygen: they are often observed to be able to maintain basic life activities when dissolved oxygen is extremely low, and some species are even able to breathe air. For example, African catfish (Clarias gariepinus) have auxiliary respiratory organs that allow them to breathe air directly when wetlands are hypoxic, thus surviving in semi-terrestrial environments. Another example is the common farmed species, channel catfish (Ictalurus punctatus), which has no specialized respiratory organs but has a strong tolerance to periodic hypoxia and can survive when dissolved oxygen drops sharply in ponds at night. Field trials have shown that catfish can still feed and grow in water bodies with dissolved oxygen levels of only about 20% of normal levels. This adaptability
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 49 makes it one of the ideal species for aquaculture in low-oxygen environments. It is worth noting that the tolerance to hypoxia varies among catfish species and populations, which is closely related to the long-term selection pressure of their living environment (Tripathi et al., 2013; Mohindra et al., 2016). This study will summarize the physiological and genomic research progress on catfish hypoxia tolerance, explore its evolutionary adaptation mechanism, analyze the main characteristics of catfish hypoxia physiological adaptation, analyze the key genes involved in hypoxia tolerance and their regulatory changes from a genomic perspective, and introduce the genomic selection signals and epigenetic responses of catfish populations in long-term hypoxia environments. This study will also introduce the progress of functional verification of hypoxia tolerance mechanisms using omics and gene editing technologies, compare the hypoxia tolerance of catfish under different species and ecological conditions through typical cases, and look forward to the prospect of applying these studies to the selection of hypoxia-tolerant varieties and the sustainable development of freshwater fisheries. This study hopes to deepen the comprehensive understanding of catfish hypoxia tolerance and provide a reference for future related research and applications. 2 Physiological Adaptation Characteristics of Catfish toHypoxia 2.1 Behavior and respiratory regulation mechanism Under hypoxia stress, fish usually take a series of behavioral adjustments to increase oxygen intake or reduce oxygen consumption. Catfish are no exception. When the dissolved oxygen in the environment decreases, catfish often first show behaviors such as decreased activity and immobility to reduce energy consumption (Wang et al., 2017; Zhong et al., 2017). At the same time, many catfish will start aquatic surface respiration (ASR): they swim to the surface of the water body, "surface" to obtain water with higher oxygen content or swallow air directly. For example, channel catfish were observed to increase the frequency of buoyancy and perform ASR when the dissolved oxygen dropped below 2 mg/L, which helped to prolong their survival time in hypoxic water. In addition, some catfish species with auxiliary respiratory organs (such as catfish) can also perform pulmonary breathing: they periodically surface to swallow air and store the air in the supragillary organs for gas exchange. When the hypoxic environment persists, catfish will also change their gill morphology and ventilation pattern. 2.2 Metabolic adaptation Under hypoxic conditions, catfish show unique metabolic regulation strategies to reduce dependence on oxygen and maintain energy balance. Studies have shown that catfish will actively reduce their basal metabolic rate when hypoxic, belonging to "oxygen-adaptive" fish, prolonging their survival time by reducing oxygen consumption. At the same time, the glycolysis pathway in their body is significantly activated: the glucose level in the blood increases, lactic acid accumulates rapidly, and the activity of enzymes such as lactate dehydrogenase increases, indicating that catfish compensate for insufficient energy supply by strengthening anaerobic glycolysis. This mechanism of obtaining ATP by enhancing glycolysis helps catfish maintain the necessary energy supply in short-term hypoxia (Xiao et al., 2024; Xing et al., 2025). In addition, a study compared the differences in the utilization preferences of energy substrates in hypoxia among different fish species and found that fish species that prefer to use carbohydrates for energy tend to have a stronger tolerance to hypoxia, while fish species that rely mainly on fat oxidation for energy have poorer tolerance (Figure 1) (Ma et al., 2023). This suggests that hypoxia-tolerant fish species such as catfish may survive hypoxia by reducing fatty acid decomposition and increasing sugar anaerobic metabolism. In fact, catfish will experience "metabolic depression" phenomena such as decreased body activity and loss of appetite when exposed to hypoxia, in order to reduce ATP consumption and oxygen demand, which is one of its important adaptive strategies (Mandic and Regan, 2018). 2.3 Regulation of cardiovascular and hemoglobin systems Catfish maintain tissue oxygen supply to the maximum extent through a series of cardiovascular adjustments such as increasing hemoglobin content, increasing the number of red blood cells, and improving circulation and microcirculation. These adaptive changes are similar to the strategies of plateau birds and mammals to increase
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 50 red blood cells under hypoxia, reflecting the convergent evolutionary characteristics of different groups to hypoxic environments (van der Weele and Jeffery, 2022). However, some studies have pointed out that the cardiovascular response patterns of different fish species vary greatly. Hypoxia-tolerant fish such as catfish may be more inclined to maintain a stable cardiac output to ensure tissue oxygen supply (Mandic and Regan, 2018). In addition to hemodynamic regulation, catfish also increase the oxygen-carrying capacity of blood at the molecular level by activating pathways such as erythropoietin (EPO). For example, studies on zebrafish have shown that upregulation of the HIF pathway can promote erythropoiesis and enhance hypoxia tolerance. It is speculated that a similar mechanism also exists in catfish: hypoxia-induced HIF-1α stabilization will promote the expression of genes such as EPO, thereby stimulating erythropoiesis (Cai et al., 2020). In addition, the hypoxic environment will also prompt the catfish body to increase the density of tissue capillaries to shorten the oxygen diffusion distance. Figure 1 Metabolic regulatory mechanisms of fish hypoxia tolerance (Adopted from Ma et al., 2023) Image caption: Fish species with low hypoxia tolerance (left) mainly rely on fatty acid β-oxidation for energy supply; fish species with high hypoxia tolerance (right) inhibit Atgl, Pparα, and Cpt1b to reduce fatty acid metabolism (Adopted from Ma et al., 2023) 3 The Basis of Hhypoxia Tolerance at the Genomic Level of Catfish 3.1 Structure and regulation of core genes of the HIF pathway The core genes of the HIF pathway play a central role in catfish's adaptation to hypoxia: they achieve transcriptional regulation of many downstream effector genes (such as hemoglobin, EPO, glycolytic enzymes, VEGF, etc.) through oxygen-dependent stability regulation. The optimization of the function and structure of HIF pathway genes in catfish during evolution helps them to quickly activate cell protection mechanisms in repeated hypoxic habitats, thereby improving hypoxia survival (Chen et al., 2020; Babin et al., 2024). Babin et al. (2024) compared the HIFα and PHD sequences of various fish and found that in fish with high hypoxia tolerance, unique mutations were fixed at certain amino acid sites of the HIF-2α protein, which changed the physicochemical properties of the protein. These variations were significantly correlated with the lower critical oxygen partial pressure (P_crit) of these fish. In addition, the HIF-3α subunit unique to aquatic animals such as catfish is also worthy of attention. A study found that knocking out the zebrafish hif-3α gene resulted in delayed red blood cell development and reduced hypoxia tolerance, indicating that HIF-3α also plays an important role in hypoxic hematopoiesis and tolerance (Cai et al., 2020).
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 51 3.2 Changes in gene families related to energy metabolism Another genomic basis for catfish hypoxia tolerance is reflected in the modification and expansion of energy metabolism-related genes. First, many fish enhance their functions by amplifying copies of certain key metabolic protein genes under long-term hypoxic stress. For example, the oxygen-carrying protein myoglobin gene in the genome of walking catfish (Clarias batrachus) has been massively amplified, with 15 copies identified, while most non-gill fish have only 1-2 copies. Enzyme genes related to catfish hypoxia metabolic pathways also show adaptive changes. During acute hypoxia, the expression of glycolysis-related enzymes such as phosphofructokinase (PFK) and pyruvate kinase (PK) in catfish is upregulated, while the expression of fructose bisphosphatase (FBP), which is in the opposite direction of gluconeogenesis, is downregulated, which promotes the anaerobic decomposition of sugars to quickly supply energy (Ma et al., 2023; Xiao et al., 2024). Some genes related to mitochondrial function and oxidative phosphorylation have also undergone functional changes in hypoxia-tolerant fish. For example, studies have reported that freshwater fish inhibit mitochondrial respiratory chain activity to reduce ROS generation during hypoxia and reoxygenation. Catfish may reduce oxygen consumption and reduce oxidative damage in hypoxia by regulating the expression of mitochondrial respiratory enzyme genes. 3.3 Antioxidant and stress response genes During the process of oxygen supply reduction and recovery, a large amount of reactive oxygen species (ROS) will be generated, causing oxidative damage to cells. Therefore, hypoxia-tolerant fish have evolved a strong antioxidant defense system. Under hypoxic stress, catfish activate a variety of antioxidant enzymes and molecular chaperone genes to reduce oxidative stress. Catfish minimizes oxidative damage caused by hypoxia by regulating antioxidant-related gene networks (including improving ROS clearance, initiating chaperone protection, and inhibiting inflammation). This efficient molecular stress response ability is also an important guarantee for its hypoxia-tolerant survival, which is highly consistent with the antioxidant adaptation observed in other hypoxia-tolerant fish (such as crucian carp, loach, etc.) (Abdel-Tawwab et al., 2019). Studies on Indian catfish have shown that hypoxia can upregulate the expression of genes such as HSP90 and HSP70, which helps stabilize the intracellular protein structure and prevent denaturation and aggregation (Mohindra et al., 2015). In addition, catfish often activate stress signaling pathways such as NF-κB when hypoxic, triggering cellular defense and repair mechanisms (Xing et al., 2025). 3.4 Evolution of the hemoglobin gene family As an oxygen transport carrier, the evolution of the hemoglobin gene family has a profound impact on the hypoxia tolerance of fish. Hemoglobin in teleost fish is usually encoded by multiple pairs of α and β subunit genes, which originated from the fish genome duplication event and underwent functional differentiation. Li et al. (2018) reported that the mRNA level of hemoglobin genes in the suprapharyngeal organs (auxiliary respiratory organs) of walking catfish was much higher than that in the gills, reflecting that the fish increased the efficiency of oxygen uptake from the air by highly expressing hemoglobin in the air breathing organs. On the other hand, the affinity and synergistic effect of hemoglobin for oxygen in different fish species vary, which is related to the amino acid sequence variation of hemoglobin genes. Hypoxia-tolerant fish often evolve hemoglobin with higher oxygen affinity so that they can more efficiently take up oxygen from water in hypoxic water environments. For example, hemoglobin mutations in many plateau fish increase oxygen affinity, thereby enhancing survival in hypoxic high-altitude environments (Borowiec et al., 2020). Although the research on the oxygen-binding properties of catfish hemoglobin is relatively limited, it is speculated that catfish may have moderate hemoglobin oxygen affinity and the ability to regulate pH by the Bohr effect so that it can maintain oxygen transport function under stress such as hypoxia and acidosis. 4 Catfish Population Genome and Adaptive Evolution to Hypoxia 4.1 Genome comparison and selection signal analysis Evidence from population genome and comparative genomics shows that the formation of catfish hypoxia tolerance involves the adaptive evolution of multiple key genes. This includes the variation and selection of
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 52 oxygen sensing pathway genes (such as the HIF axis), oxygen transport and stress defense genes (such as hemoglobin, heat shock protein, etc.). These changes at the gene level enable catfish populations to optimize survival and reproduction in different oxygen-containing environments, and record the imprint of natural selection from the changes in gene frequency (Kang et al., 2017; Babin et al., 2024). RAD-seq analysis of high-altitude and low-altitude catfish populations in the Nujiang River Basin in China found that there were significant allele frequency differences between high-altitude tributary populations and low-altitude main stream populations at several gene loci. These differential loci are enriched in functional categories such as multicellular organism development and cell metabolism, showing traces of selection related to adaptation to hypoxic environments. Further comparison of these candidate genes with a list of 1 351 known hypoxia-related genes revealed that several of them (such as SENP3, BMPR2, DNAJB5, etc.) are key genes involved in hypoxia response and oxygen balance regulation (Kang et al., 2017). 4.2 Epigenetic regulatory mechanism The epigenetic mechanism provides catfish with another flexible means of adapting to hypoxia, enabling them to make reversible gene expression adjustments during their individual life course according to changes in environmental oxygen levels, and may pass on the beneficial effects of these adjustments to offspring, thereby fixing them in the population (Abdelnour et al., 2024; Johnston et al., 2025). Studies have found that some epigenetic enzymes themselves are sensitive to oxygen concentrations. For example, TET dioxygenases responsible for removing DNA methylation and JmjC domain proteins that mediate histone demethylation both require molecular oxygen as a cofactor. In anoxic environments, the activity of these enzymes decreases, which may lead to a decrease in 5-hydroxymethylcytosine (5hmC) in the promoter region of genes or an increase in the level of histone hypermethylation, thereby affecting the expression of related genes (Johnston et al., 2025). For species such as catfish that live in seasonally hypoxic waters for a long time, their genomes may accumulate adaptive epigenetic characteristics. For example, hypoxia-tolerant fish may respond quickly to energy crises by reducing DNA methylation in the promoters of key metabolic genes and increasing their expression in hypoxia. 4.3 Evolutionary dynamics of gene-environment interactions Gene-environment interactions play a central role in the evolution of catfish hypoxia tolerance: environmental hypoxia shapes the direction of gene selection, and the presence of genetic variation determines how quickly and to what extent fish can adapt to new oxygen-containing conditions. This feedback mechanism ensures that catfish populations can continuously optimize their tolerance strategies as the environment changes, achieving a dynamic match between gene frequency and habitat (Mandic and Regan, 2018; Yu et al., 2021). For example, artificial hybrids of African catfish and closely related species were found to have stronger environmental tolerance, including improved tolerance to hypoxia. Hybridization recombines genes from different ecological backgrounds, which may produce some genotypes that are more adaptable to extreme environments than purebreds, thus providing raw materials for breeding and adaptive evolution (Nguinkal et al., 2024). 5 Experimental Research and Functional Validation Progress 5.1 Transcriptomics and metabolomics combined analysis reveals hypoxia stress response pathways Omics technology is advancing the study of catfish hypoxia adaptation to the system level, not only verifying the important position of previous candidate genes such as HIF and sugar metabolism enzymes, but also discovering new participants such as immune and signaling pathways. These studies are of great significance in guiding genetic breeding and molecular improvement of hypoxia-tolerant varieties (Yang et al., 2018; Mu et al., 2020). Taking channel catfish as an example, Yang et al. (2018) conducted transcriptome analysis on the swim bladder tissue of adult and juvenile fish under hypoxia and normoxic conditions, and identified 155 genes in adult fish and 2 127 genes in juvenile fish whose expression was significantly changed under hypoxia. Pathway enrichment analysis showed that these differentially expressed genes were significantly enriched in the HIF signaling pathway and the MAPK, PI3K/Akt/mTOR, Ras, and VEGF cascade pathways. Metabolomics can measure changes in metabolite concentrations in fish, providing direct evidence for analyzing energy metabolism reconstruction under
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 53 hypoxia. Combining transcriptome and metabolome analysis can correspond changes in gene expression to changes in metabolic flux, revealing the regulatory mechanism in more depth. 5.2 CRISPR/Cas9-mediated functional gene knockout experiments to verify key sites Functional genomics, especially CRISPR/Cas9 gene editing technology, provides a powerful tool for verifying the key genes and sites of catfish hypoxia tolerance. Although there are relatively few gene knockout experiments in aquatic fish such as catfish, studies on other model fish have shown that targeted knockout of hypoxia-responsive genes can significantly affect the hypoxia-tolerant phenotype. For example, HIF-1α and HIF-3α in zebrafish are core transcription factors that regulate hypoxia response. By knocking out the zebrafish hif-3α gene through CRISPR/Cas9, researchers observed that the mutant fish had impaired erythropoiesis and reduced hemoglobin, resulting in a significantly shortened survival time in hypoxic water. This result directly proves the functional importance of HIF-3α to fish hypoxia tolerance (Cai et al., 2020). Similarly, site-directed mutagenesis of the zebrafish pVHL gene can simulate the natural variation of plateau fish pVHL. The results showed that zebrafish with plateau mutations showed stronger HIF signaling activity and hypoxia tolerance. This shows that mutations at certain key sites on the pVHL protein can improve HIF stability, thereby enhancing hypoxia adaptability (Chen et al., 2020). 5.3 Phenotype-gene association analysis under simulated hypoxia experimental system Phenotype-gene association analysis under simulated hypoxic environment provides an effective path to reveal the complex traits of catfish hypoxia tolerance. It is not limited to single gene effects, but captures the combined effects of multiple genes and pathways, which is closer to the real biological situation. With the application of more high-resolution molecular markers and the testing of larger population samples, it is expected to depict the genetic architecture map of catfish hypoxia tolerance traits and identify markers and sites that can be used for molecular breeding (Yu et al., 2021). It is reported that when channel catfish are exposed to hypoxia at night, the expression of genes related to feeding and stress in their hypothalamus changes in circadian rhythm, affecting feeding behavior and physiological state. This transcriptional response to environmental changes is also related to the individual's genotype: some individuals may have "pre-adaptive" gene expression regulation, which prepares them before the onset of hypoxia, thereby showing stronger tolerance. This hypothesis can be tested by comparing the expression profiles of individuals with different tolerance. 6 Case Analysis of the Evolution of Catfish's Tolerance to Hypoxia 6.1 Study on the evolution of hypoxia tolerance in representative catfish species Catfish are a group with extremely high species diversity, and several representative species are known for their excellent tolerance to hypoxia, making them ideal models for studying hypoxia adaptation. For example, the American channel catfish (Ictalurus punctatus, commonly known as "channel catfish" in Chinese) is an important species for freshwater aquaculture in North America. It can survive in high-density aquaculture ponds with significantly reduced dissolved oxygen at night. This ecological success is attributed to the channel catfish's strong hypoxia-tolerant genotype: studies have pointed out that the reason why channel catfish is widely cultured is partly because it has a "relatively high tolerance to hypoxia" compared to other catfish (Yang et al., 2018). The walking catfish in Asia (such as Clarias batrachus, commonly known as "crawling catfish") is also known for its ability to "walk" on land. They often live in low-oxygen rice fields and shallow ponds. When the original water body dries up, they can rely on their pectoral fins to support their bodies and crawl forward to find new water sources. Walking catfish has the ability to breathe through gills and air through suprapharyngeal organs, and is a "double champion" in tolerance to hypoxia and drought. Its whole genome sequencing study revealed that this fish has particularly amplified genes related to oxygen storage and utilization (such as myoglobin), and has adapted to terrestrial life by enhancing hemoglobin expression and angiogenesis (Li et al., 2018). In addition, other catfish species, such as the armored catfish in South America, also show tolerance to hypoxia, and they can use the intestine to breathe air in hypoxic rivers. Physiological studies on these species have shown that even if the strategies in heart rate, ventilation and other responses are different, their adaptation principles of increasing oxygen uptake and reducing oxygen consumption are consistent (Scott et al., 2017).
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 54 6.2 Comparative study on the adaptation of catfish populations in different ecological regions to hypoxia Catfish are distributed in rivers, lakes, swamps and artificial breeding environments. There are obvious differences in the ability of catfish populations in different habitats to tolerate hypoxia. This difference has both a genetic basis and the contribution of environmental plasticity factors. Comparison of catfish hypoxia tolerance in river and lake environments reflects the important influence of hydrodynamics and oxygen conditions. In aquaculture environments, different management conditions and ecological patterns affect catfish oxygen tolerance. High-density pond culture often causes hypoxia in the early morning due to the consumption of oxygen by algae and microorganisms at night. Catfish populations that have been in this environment for a long time may have increased their hypoxia tolerance threshold through phenotypic plasticity (Figure 2) (Kumar et al., 2018). Figure 2 An intensively aerated commercial catfish pond in Mississippi (Adopted from Kumar et al., 2018) Catfish populations in different geographical regions have different hypoxia tolerance due to long-term exposure to different climatic and hydrological conditions. Tropical regions have high water temperatures, high biological oxygen consumption, and more frequent hypoxia stress on fish, so catfish there tend to be more "tolerant" than populations in temperate regions. For example, bearded catfish in tropical freshwater environments in Africa generally have excellent hypoxia tolerance, which is related to the fact that the ponds they inhabit are often hypoxic at night. In contrast, channel catfish in large lakes in temperate North America rarely encounter extreme hypoxia, and their tolerance may not be as good as the former. Through cross-population hybridization and introduction, the genetic oxygen tolerance differences of catfish of different lineages can be compared. For example, the hypoxia survival rate and related physiological indicators of the hybrids can be observed by hybridizing African catfish with strong hypoxia tolerance and local catfish (Kang et al., 2017; Borowiec et al., 2018). 7 Application Prospects and Research Prospects 7.1 Hypoxia-tolerant breeding strategies and molecular marker screening In the field of aquaculture, it is of great significance to improve the hypoxia tolerance of cultured varieties. The genetic improvement of hypoxia tolerance in catfish can be started from two aspects: traditional breeding and modern molecular assisted breeding. On the one hand, traditional family selection has been used to screen catfish strains with strong stress resistance. It is reported that after artificial selection, several cultured strains of American channel catfish have increased their hypoxia tolerance survival time by about 20%-30% compared with unselected wild strains (Sun et al., 2014; Wang et al., 2017). On the other hand, molecular marker-assisted breeding and whole genome selection provide more efficient means for the improvement of hypoxia tolerance traits. The breeding of hypoxia-tolerant catfish varieties requires the comprehensive use of traditional and modern technical means: there must be a pressure selection process of repeated screening in a hypoxic environment, and it is also necessary to be good at using molecular markers to lock in dominant genes. With the advancement of catfish whole genome sequencing and functional genomics research, a series of molecular markers related to hypoxia
International Journal of Molecular Zoology, 2025, Vol.15, No.2, 48-57 http://animalscipublisher.com/index.php/ijmz 55 tolerance will be discovered and used in breeding practice, accelerating the breeding of new strains with stronger adaptability (Yu et al., 2021; Nguinkal et al., 2024). 7.2 Adaptation strategies for freshwater fisheries to climate change Coping with the hypoxia challenge brought about by climate change requires both technology and management: both "hypoxia-tolerant fish" and "high oxygen water" should be cultivated. Only in this way can freshwater fisheries maintain stable production and income under more severe environmental conditions in the future (Galappaththi et al., 2021; Sampaio et al., 2021). In aquaculture management, water oxygenation and water quality improvement measures should be actively taken. At the same time, reducing the degree of eutrophication through the cultivation of aquatic plants or the introduction of microbial preparations can also help reduce the risk of hypoxia. Secondly, selecting and cultivating varieties with stronger resistance to hypoxia is the key to improving adaptability from the source. In addition, it is also very important to strengthen the monitoring and early warning of dissolved oxygen in water bodies. IoT sensing technology can be used to monitor the dissolved oxygen level of aquaculture water and natural waters in real time. Once the oxygen concentration is detected to drop to a critical value, emergency plans can be immediately initiated, such as temporary transfer of farmed fish, local water spraying and oxygenation, etc., to avoid serious losses. From a more macro perspective, mitigating climate change and protecting wetland ecosystems are also fundamental measures to maintain water oxygen content and fishery sustainability (Muringai et al., 2022). 7.3 Cross-species comparison and evolutionary enlightenment of basic research The research value of catfish's hypoxia tolerance has surpassed the species itself. Through comparative studies with other species, the "evolutionary blueprint" of life systems against hypoxia challenges is gradually drawn. This is not only an important topic in ecology and evolutionary biology, but will also have a profound impact on aquaculture, environmental protection, and human health (van der Weele and Jeffery, 2022; Babin et al., 2024). By comparing catfish with other hypoxia-tolerant species (such as crucian carp, loach, blind cave fish, etc.) and species with limited hypoxia tolerance, researchers can extract common mechanisms and evolutionary trends of life systems in response to hypoxia stress. In addition, some unique adaptation "innovations" can be discovered through cross-species comparisons. For example, catfish have evolved air breathing and myoglobin expansion, which most fish do not have; while eels and others have evolved the ability to reduce metabolism and enter a dormant state when hypoxia occurs, which catfish do not have. Comparing these differences helps to understand the diverse strategies of organisms to deal with hypoxia in different evolutionary backgrounds, as well as the fit between these strategies and their respective ecological environments (Mandic and Regan, 2018). Looking forward to the future, as sequencing costs decrease, more genomes of hypoxia-tolerant and hypoxia-intolerant species will be compared, and conserved factors and mutation sites directly related to hypoxia adaptation will be accurately located. Acknowledgments We would like to thank the research team for their suggestions on my manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Abdelnour S.A., Naiel M.A., Said M.B., Alnajeebi A.M., Nasr F.A., Al-Doaiss A.A., El-Sherbiny M., Abdel-Razek A.G., and Noreldin A.E., 2024, Environmental epigenetics: Exploring phenotypic plasticity and transgenerational adaptation in fish, Environmental Research, 234: 118799. https://doi.org/10.1016/j.envres.2024.118799 Abdel-Tawwab M., Monier M.N., Hoseinifar S.H., and Faggio C., 2019, Fish response to hypoxia stress: Growth, physiological, and immunological biomarkers, Fish Physiology and Biochemistry, 45(4): 997-1013. https://doi.org/10.1007/s10695-019-00680-1 Babin C.H., Leiva F.P., Verberk W.C., and Rees B.B., 2024, Evolution of key oxygen-sensing genes is associated with hypoxia tolerance in fishes, Genome Biology and Evolution, 16(9): evae183. https://doi.org/10.1093/gbe/evae183
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International Journal of Molecular Zoology, 2025, Vol.15, No.2, 58-68 http://animalscipublisher.com/index.php/ijmz 58 Review and Progress Open Access The Evolutionary Genomics of Giant African Land Snail (Lissachatina fulica): Insights from Whole-Genome Sequencing and Structural Variations Wei Liu 1, JiaChen2 1 Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China 2 Tropical Animal Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: jia.chen@hitar.org International Journal of Molecular Zoology, 2025, Vol.15, No.2 doi: 10.5376/ijmz.2025.15.0007 Received: 15 Feb., 2025 Accepted: 07 Mar., 2025 Published: 18 Mar., 2025 Copyright © 2025 Liu and Chen, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Liu W., and Chen J., 2025, The evolutionary genomics of giant African land snail (Lissachatina fulica): insights from whole-genome sequencing and structural variations, International Journal of Molecular Zoology, 15(2): 58-68 (doi: 10.5376/ijmz.2025.15.0007) Abstract The giant African land snail (Lissachatina fulica) has an extremely strong invasive ability, threatening agricultural and forestry production and posing public health risks. This study, based on whole-genome sequencing and structural variation (SV) analysis, explored its evolutionary genomic characteristics. The functional annotation results show that, the gene families related to carbohydrate metabolism, mucus synthesis, and shell biominalization have expanded. These changes clearly provide support for its survival in diverse environments. Comparative genomics further discovered that, it shared a genome-wide replication event with Achatina immaculata that occurred approximately 70 million years ago. This event might have promoted its ecological adaptation and terrestrial biochemical processes. SV plays a crucial role in regulating gene expression, enhancing environmental tolerance, immune defense and resource utilization. At the same time, it can also serve as a phylogenetic and biogeographic marker to track its invasion path. The study emphasizes that in the future, pan-genomic and large-scale population studies based on SV should be given priority, which will help to gain a deeper understanding of its evolutionary and adaptive mechanisms. Keywords Giant African land snail (Lissachatina fulica); Whole genome; Structural variation; Gene family expansion; Biosafety 1 Introduction The giant African land snail (Lissachatina fulica) first lived in East Africa. But it has now traveled a long distance - it can be seen in many places in Asia, the Pacific, the Caribbean, Latin America, and even Europe, and is distributed in more than 50 countries (Vijayan et al., 2020; 2022; Gabetti et al., 2023). At the beginning, people placed it in the genus Achatina, so its name was Achatina fulica. Later, some scholars conducted morphological and molecular phylogenetic analyses and concluded that it was a separate branch within the genus Achatina. Therefore, it was renamed Lissachatina fulica (Guo et al., 2019). This kind of snail has a strong adaptability, spreads rapidly, has a high reproductive capacity, and can survive in any environment - whether in cities, farmlands, or protected areas (Vazquez et al., 2018; Gabetti et al., 2023; Castillo et al., 2025). What's more troublesome is that, it is hermaphroditic and can self-fertilize, and one individual may establish a new population (Vazquez et al., 2018; Gabetti et al., 2023). L. fulica is not friendly to biodiversity. It will push out local mollusks, leading to the rapid decline of some endemic snail populations. This situation is particularly obvious on islands (Gerlach et al., 2020; Gabetti et al., 2023; Castillo et al., 2025). In farmlands, its reputation is even worse. It is notorious as a pest - crops, vegetables, and horticultural plants are all gnawed, causing significant economic losses (Morrison et al., 2015; Ayyagari and Sreerama, 2017). The troubles do not end here. It is also a transmitter of some zoonotic parasites, like Angiostrongylus cantonensis, which causes public health problems in invaded areas (Vazquez et al., 2018; Gabetti et al., 2023). Whole-genome sequencing provides a comprehensive view of the genetic diversity, population structure, and evolutionary history of invasive species like L. fulica (Morrison et al., 2015). This approach identify key genetic markers, such as microsatellite markers, to help track invasion pathways, understand population dynamics events,
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