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Naeem Z, Zuberi A, Ali M, Naeem AD, Naeem M. An approach to optimizing dietary protein to growth and body composition in walking catfish, Clarias batrachus (Linneaeus, 1758). PLoS One 2024; 19:e0301712. [PMID: 38701105 PMCID: PMC11068203 DOI: 10.1371/journal.pone.0301712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/20/2024] [Indexed: 05/05/2024] Open
Abstract
Clarias batrachus is a commercially important food fish. In the present study, effect of varying dietary protein levels was evaluated on the survival, growth parameters and proximate composition of C. batrachus. Diets comprising 25%, 30%, 35%, 40%, 45%, and 50% crude protein (CP) were supplied to fish in T1, T2, T3, T4, T5, and T6, respectively, at the rate of 5% of fish body weight for the entire 90 days, twice daily. Size of each stocked C. batrachus was recorded after 15 days. Results revealed 100% survival rate of C. batrachus in all treatments. Significantly highest (P<0.001) mean value of weight gain (g/fish), percent weight gain, daily growth rate, specific growth rate and protein efficiency ratio (PER) in C. batrachus were recorded, reared in T4 by feeding 40% CP in diet. The best FCR value (1.90±0.02) for C. batrachus was obtained in T4 by feeding 40%CP in diet. Mean value of water, ash, fat and protein contents (wet mass) were ranged 74.10-79.23%, 3.12-4.68%, 3.90-4.43% and 13.09-16.79% for C. batrachus in the studied treatment groups. Water content (%) was found significantly (P<0.05) higher in the body of C. batrachus for T1, T2, T3 and T6 than for T4 and T5. Ash was found significantly (P<0.05) higher in the fish reared in T4 and T5. Fat content in the wet body mass of C. batrachus was found significantly higher in T4 and T1. While, significant higher (P<0.05) values of mean protein content was noted in C. batrachus reared in T4 and T5. Body composition of C. batrachus was also categorically affected by body size, however, condition factor showed non-significant correlation in most of the relationships in the present study. Overall, results indicated that feeding appropriate diet (containing 40% CP) to the fish resulted good growth performance, lower FCR and higher protein content in the fish. Present study provides valuable knowledge of optimal dietary protein level in C. batrachus which will help in commercial success of aquaculture.
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Affiliation(s)
- Zara Naeem
- Fisheries and Aquaculture Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Amina Zuberi
- Fisheries and Aquaculture Program, Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ali
- Vice Chancellor, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Muhammad Naeem
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
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Han C, Yang G, Zhang H, Peng H, Yang J, Zhu P, Zou J, Wang P. Development and validation of genome-wide SSR molecular markers of Tapes dorsatus. Mol Biol Rep 2024; 51:73. [PMID: 38175290 DOI: 10.1007/s11033-023-08949-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/24/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Tapes dorsatus is an economically important benthic animal in the Beibu Gulf of China. However, the deficiency of microsatellite markers has hindered the study of its genetics. The development of microsatellite markers will provide useful tools for genetic improvement, variety identification, phylogenetic analysis and resource conservation. METHODS AND RESULTS Within the genome sequence, 145,008 simple sequence repeats (SSRs) were identified, and 29,691 primer pairs were designed successfully. A total of 100 primer pairs were randomly synthesized for testing, and 93 primers yielded products. Sixty highly polymorphic primers were used to reveal the genetic diversity of 50 T. dorsatus individuals. The average number of alleles (Na) of the population was 10.40; the average number of effective alleles was 6.16, the average expected heterozygosity (He) was 0.82, and the average polymorphic information content was 0.80. The genetic structure of the population was detected, by which the population could be divided into three subpopulations. CONCLUSION We identified 145,008 SSRs in the genome of T. dorsatus and designed 29,691 primer pairs in this study. Of 100 synthesized primers, 60 were highly polymorphic and used to reveal the genetic diversity and structure of the population. The SSR markers identified here will provide useful tools and a foundation for genetic diversity, linkage mapping and molecular marker-aided breeding in T. dorsatus.
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Affiliation(s)
- Chunli Han
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China.
| | - Guohao Yang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Huiling Zhang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Huijing Peng
- Guangxi Institute of Oceanology, Beihai, 536000, China
| | - Jialin Yang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Peng Zhu
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China
| | - Jie Zou
- Guangxi Institute of Oceanology, Beihai, 536000, China.
| | - Pengliang Wang
- College of Marine Science, Beibu Gulf University, Qinzhou, 535011, Guangxi, China.
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Baisvar VS, Kushwaha B, Kumar R, Kumar MS, Singh M, Rai A, Sarkar UK. BAC-FISH Based Physical Map of Endangered Catfish Clarias magur for Chromosome Cataloguing and Gene Isolation through Positional Cloning. Int J Mol Sci 2022; 23:ijms232415958. [PMID: 36555603 PMCID: PMC9781557 DOI: 10.3390/ijms232415958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Construction of a physical chromosome map of a species is important for positional cloning, targeted marker development, fine mapping of genes, selection of candidate genes for molecular breeding, as well as understanding the genome organization. The genomic libraries in the form of bacterial artificial chromosome (BAC) clones are also a very useful resource for physical mapping and identification and isolation of full-length genes and the related cis acting elements. Some BAC-FISH based studies reported in the past were gene based physical chromosome maps of Clarias magur (magur) to understand the genome organization of the species and to establish the relationships with other species in respect to genes' organization and evolution in the past. In the present study, we generated end sequences of the BAC clones and analyzed those end sequences within the scaffolds of the draft genome of magur to identify and map the genes bioinformatically for each clone. A total of 36 clones mostly possessing genes were identified and used in probe construction and their subsequent hybridization on the metaphase chromosomes of magur. This study successfully mapped all 36 specific clones on 16 chromosome pairs, out of 25 pairs of magur chromosomes. These clones are now recognized as chromosome-specific makers, which are an aid in individual chromosome identification and fine assembly of the genome sequence, and will ultimately help in developing anchored genes' map on the chromosomes of C. magur for understanding their organization, inheritance of important fishery traits and evolution of magur with respect to channel catfish, zebrafish and other species.
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Affiliation(s)
- Vishwamitra Singh Baisvar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Basdeo Kushwaha
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Ravindra Kumar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
- Correspondence:
| | - Murali Sanjeev Kumar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Mahender Singh
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR—Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi 110012, India
| | - Uttam Kumar Sarkar
- ICAR—National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226002, India
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Behera BK, Parhi J, Dehury B, Rout AK, Khatei A, Devi AL, Mandal SC. Molecular characterization and structural dynamics of Aquaporin1 from walking catfish in lipid bilayers. Int J Biol Macromol 2021; 196:86-97. [PMID: 34914911 DOI: 10.1016/j.ijbiomac.2021.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 01/17/2023]
Abstract
Aquaporin's (AQPs) are the major superfamily of small integral membrane proteins that facilitates transportation of water, urea, ammonia, glycerol and ions across biological cell membranes. Despite of recent advancements made in understanding the biology of Aquaporin's, only few isoforms of aquaporin 1 (AQP1) some of the teleost fish species have been characterized at molecular scale. In this study, we made an attempt to elucidate the molecular mechanism of water transportation in AQP1 from walking catfish (Clarias batrachus), a model species capable of breathing in air and inhabits in challenging environments. Using state-of-the-art computational modelling and all-atoms molecular dynamics simulation, we explored the structural dynamics of full-length aquaporin 1 from walking catfish (CbAQP1) in lipid mimetic bilayers. Unlike AQP1 of human and bovine, structural ensembles of CbAQP1 from MD revealed discrete positioning of pore lining residues at the intracellular end. Snapshots from MD simulation displayed differential dynamics of aromatic/arginine (ar/R) filter and extracellular loop C bridging transmembrane (TM) helix H3 and H4. Distinct conformation of large extracellular loops, loop bridging TM2 domain and HB helix along with positioning of selectivity filter lining residues controls the permeability of water across the bilayer. Moreover, the identified unique and conserved lipid binding sites with 100% lipid occupancy signifies lipid mediated structural dynamics of CbAQP1. All-together, this is the first ever report on structural-dynamics of aquaporin 1 in walking catfish which will be useful to understand the molecular basis of transportation of water and other small molecules under varying degree of hyperosmotic environment.
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Affiliation(s)
- Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India.
| | - Janmejay Parhi
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
| | - Budheswar Dehury
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India; Department of Chemistry, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata 700120, India
| | - Ananya Khatei
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
| | - Asem Lembika Devi
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
| | - Sagar Chandra Mandal
- Department of Fish Genetics and Reproduction, College of Fisheries, Central Agricultural University (Imphal), Lembucherra, Tripura West, Tripura 799210, India
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Patturaj M, Munusamy A, Kannan N, Kandasamy U, Ramasamy Y. Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation. Genomics Inform 2021; 19:e33. [PMID: 34638180 PMCID: PMC8510864 DOI: 10.5808/gi.21031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022] Open
Abstract
Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%–62.5%), followed by tri- (23.7%–27.2%), tetra- (5.2%–5.6%), penta- (5.0%–5.3%), and hexa-nucleotide (2.7%–2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.
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Affiliation(s)
- Maheswari Patturaj
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
| | - Aiswarya Munusamy
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
| | | | | | - Yasodha Ramasamy
- Institute of Forest Genetics and Tree Breeding, Coimbatore 641002, India
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Individual chromosome identification in Clarias magur using BAC-FISH and comparative genes analyses. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00344-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Substantial enhancement of high polymorphic SSR marker development using in silico method from 18 available rice blast fungus genome sequences and its application in genetic diversity assessment. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00264-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Li N, Bao L, Zhou T, Yuan Z, Liu S, Dunham R, Li Y, Wang K, Xu X, Jin Y, Zeng Q, Gao S, Fu Q, Liu Y, Yang Y, Li Q, Meyer A, Gao D, Liu Z. Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. BMC Genomics 2018; 19:952. [PMID: 30572844 PMCID: PMC6302426 DOI: 10.1186/s12864-018-5355-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/09/2018] [Indexed: 11/22/2022] Open
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. Electronic supplementary material The online version of this article (10.1186/s12864-018-5355-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ning Li
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lisui Bao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoyan Xu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sen Gao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qiang Fu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yang Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yujia Yang
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qi Li
- Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Dongya Gao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
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