1
|
Marnis H, Syahputra K, Iswanto B, Cartealy IC, Sularto, Darmawan J, Hayuningtyas EP, Hidayat R, Tirta Subangkit A, Arianto. The complete mitochondrial genome of the blackskin catfish ( Clarias meladerma: Clariidae) from Rokan River, Riau, Indonesia. Mitochondrial DNA B Resour 2024; 9:1093-1097. [PMID: 39165382 PMCID: PMC11334743 DOI: 10.1080/23802359.2024.2392742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 08/10/2024] [Indexed: 08/22/2024] Open
Abstract
Clarias meladerma Bleeker, 1846, a native catfish species in Indonesia belonging to the family Clariidae. The present study the complete mitochondrial genome sequence of C. meladerma from the Rokan River was sequenced by using next-generation sequencing, and its phylogenetic relationship was analyzed. The mitochondrial genome comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a total length of 16,808 bp. The mitogenome of C. meladerma exhibits a base composition of 32.49% adenine, 25.75% thymine, 14.51% guanine, and 27.25% cytosine. Phylogenetic analysis indicated that C. meladerma has the same clade with C. macrocephalus, C. batrachus, and C. fucus. In essence, the findings of this study lay down a genetic foundation for future investigations into C. meladerma.
Collapse
Affiliation(s)
- Huria Marnis
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Khairul Syahputra
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Bambang Iswanto
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Imam Civi Cartealy
- Research Center for Computation, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Sularto
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Jadmiko Darmawan
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | | | - Rahmat Hidayat
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Arsad Tirta Subangkit
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Arianto
- Research Center for Fishery, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| |
Collapse
|
2
|
Liu K, Xie N, Wang Y, Liu X. The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:907-917. [PMID: 37661218 DOI: 10.1007/s10126-023-10248-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Long-read sequencing technologies can generate highly contiguous genome assemblies compared to short-read methods. However, their higher cost often poses a significant barrier. To address this, we explore the utilization of mapping-based genome assembly and reference-guided assembly as cost-effective alternative approaches. We assess the efficacy of these approaches in improving the contiguity of Clarias batrachus and Culter alburnus draft genomes. Our findings demonstrate that employing an iterative mapping strategy leads to a reduction in assembly errors. Specifically, after three iterations, the Mismatches per 100 kbp value for the C. batrachus genome decreased from 2447.20 to 2432.67, reaching a minimum of 2422.67 after two iterations. Additionally, the N50 value for the C. batrachus genome increased from 362,143 to 1,315,126 bp, with a maximum of 1,315,403 bp after two iterations. Furthermore, we achieved Mismatches per 100 kbp values of 3.70 for the reference-guided assembly of C. batrachus and 0.34 for C. alburnus. Correspondingly, the N50 value for the C. batrachus and C. alburnus genomes increased from 362,143 bp and 3,686,385 bp to 2,026,888 bp and 43,735,735 bp, respectively. Finally, we successfully utilized the improved C. batrachus and C. alburnus genomes to compare genome studies using the combined approach of Ragout and Ragtag. Through a comprehensive comparative analysis of mapping-based and reference-guided genome assembly methods, we shed light on the specific contributions of reference-guided assembly in reducing assembly errors and improving assembly continuity and integrity. These advancements establish reference-guided assembly and the utilization of in silico libraries as a promising and suitable approach for comparative genomics studies.
Collapse
Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Yuxi Wang
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Xinyi Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| |
Collapse
|
3
|
Mitochondriomics of Clarias Fishes (Siluriformes: Clariidae) with a New Assembly of Clarias camerunensis: Insights into the Genetic Characterization and Diversification. Life (Basel) 2023; 13:life13020482. [PMID: 36836839 PMCID: PMC9960581 DOI: 10.3390/life13020482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The mitogenome of an endemic catfish Clarias camerunensis was determined from the Cameroon water. This circular mitogenome was 16,511 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a single AT-rich control region. The heavy strand accommodates 28 genes, whereas the light strand is constituted by ND6 and eight transfer RNA (tRNA) genes. The C. camerunensis mitochondrial genome is AT biased (56.89%), as showcased in other Clarias species. The comparative analyses revealed that most of the Clarias species have 6 overlapping and 11 intergenic spacer regions. Most of the PCGs were initiated and terminated with the ATG start codon and TAA stop codon, respectively. The tRNAs of C. camerunensis folded into the distinctive cloverleaf secondary structure, except trnS1. The placement of the conserved domains in the control region was similar in all the Clarias species with highly variable nucleotides in CSB-I. Both maximum likelihood and Bayesian-based matrilineal phylogenies distinctly separated all Clarias species into five clades on the basis of their known distributions (South China, Sundaland, Indochina, India, and Africa). The TimeTree analysis revealed that the two major clades (Indo-Africa and Asia) of Clarias species might have diverged during the Paleogene (≈28.66 MYA). Our findings revealed the separation of Indian species (C. dussumieri) and African species (C. camerunensis and Clarias gariepinus) took place during the Paleogene, as well as the South Chinese species (Clarias fuscus) and Sundaland species (Clarias batrachus) splits from the Indochinese species (Clarias macrocephalus) during the Neogene through independent colonization. This pattern of biotic relationships highlights the influence of topography and geological events in determining the evolutionary history of Clarias species. The enrichment of mitogenomic data and multiple nuclear loci from their native range or type locality will confirm the true diversification of Clarias species in African and Asian countries.
Collapse
|
4
|
Wang H, Su B, Butts IAE, Dunham RA, Wang X. Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies. Gigascience 2022; 11:6636942. [PMID: 35809049 PMCID: PMC9270728 DOI: 10.1093/gigascience/giac070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/24/2022] [Accepted: 06/16/2022] [Indexed: 12/17/2022] Open
Abstract
Background The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. Results The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. Conclusions We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish.
Collapse
Affiliation(s)
- Haolong Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.,Alabama Agricultural Experiment Station, Auburn, AL 36849, USA
| | - Baofeng Su
- Alabama Agricultural Experiment Station, Auburn, AL 36849, USA.,School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ian A E Butts
- Alabama Agricultural Experiment Station, Auburn, AL 36849, USA.,School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rex A Dunham
- Alabama Agricultural Experiment Station, Auburn, AL 36849, USA.,School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.,Alabama Agricultural Experiment Station, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| |
Collapse
|
5
|
Huang S, Yang L, Zhang L, Sun B, Gao J, Chen Z, Zhong L, Cao X. Endogenic upregulations of HIF/VEGF signaling pathway genes promote air breathing organ angiogenesis in bimodal respiration fish. Funct Integr Genomics 2021; 22:65-76. [PMID: 34839401 DOI: 10.1007/s10142-021-00822-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022]
Abstract
Air-breathing has evolved independently serval times with a variety of air-breathing organs (ABOs) in fish. The physiology of the air-breathing in bimodal respiration fish has been well understood, while studies on molecular mechanisms of the character are very limited. In the present study, we first determined the gill indexes of 110 fish species including 25 and 85 kinds of bimodal respiration fishes and non-air-breathing fishes, respectively. Then combined with histological observations of gills and ABOs/non-ABOs in three bimodal respiration fishes and two non-air breathing fishes, we found that the bimodal respiration fish was always of a degeneration gill and a well-vascularized ABO. Meanwhile, a comparative transcriptome analysis of posterior intestines, namely a well vascularized ABO in Misgurnus anguillicaudatus and a non-ABO in Leptobotia elongata, was performed to expound molecular variations of the air-breathing character. A total of 5,003 orthologous genes were identified. Among them, 1,189 orthologous genes were differentially expressed, which were enriched in 14 KEGG pathways. More specially, the expressions of hemoglobin genes and various HIF/VEGF signaling pathway genes were obviously upregulated in the ABO of M. anguillicaudatus. Moreover, we found that HIF-1α, VEGFAa, and MAP2K1 were co-expressed dramatically higher in ABOs of bimodal respiration fishes than those of non-ABOs of non-air-breathing fishes. These results indicated that the HIF/VEGF pathway played an important role in ABO angiogenesis/formation to promote fish to do aerial respiration. This study will contribute to our understanding of molecular mechanisms of air-breathing in fish.
Collapse
Affiliation(s)
- Songqian Huang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, No.1 Shizishan Stress, Hongshan District, Wuhan, 430070, Hubei Province, China.,Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, the University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Lijuan Yang
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, No.1 Shizishan Stress, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Li Zhang
- College of Marxism, Shanghai University of Finance and Economics, Shanghai, 200433, China
| | - Bing Sun
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, No.1 Shizishan Stress, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Jian Gao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, No.1 Shizishan Stress, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Zijian Chen
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, No.1 Shizishan Stress, Hongshan District, Wuhan, 430070, Hubei Province, China.,National Demonstration Center for Experimental Aquaculture Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Zhong
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, NO.173 Baishazhou Avenue, Hongshan District, Wuhan, 430207, Hubei Province, China.
| | - Xiaojuan Cao
- College of Fisheries, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, No.1 Shizishan Stress, Hongshan District, Wuhan, 430070, Hubei Province, China.
| |
Collapse
|
6
|
Ma X, Su B, Bangs M, Alston V, Backenstose NJC, Simora RM, Wang W, Xing D, Li S, Ye Z, Moss AG, Duong TY, Wang X, Dunham RA. Comparative Genomic and Transcriptomic Analyses Revealed Twenty-Six Candidate Genes Involved in the Air-Breathing Development and Function of the Bighead Catfish Clarias macrocephalus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:90-105. [PMID: 33113010 DOI: 10.1007/s10126-020-10005-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
The bighead catfish (Clarias macrocephalus) and channel catfish (Ictalurus punctatus) are freshwater species in the Siluriformes order. C. macrocephalus has both gills and modified gill structures serving as an air-breathing organ (ABO), while I. punctatus does not possess such an organ, and cannot breathe in air, providing an excellent model for studying the molecular basis of ABO development in teleost fish. To investigate the critical time window for the development of air-breathing function, seven development stages were selected based on hypoxia challenge results, and RNA-seq was performed upon C. macrocephalus to compare with the non-air-breathing I. punctatus. Five-hundred million reads were generated and 25,239 expressed genes were annotated in C. macrocephalus. Among those, 8675 genes were differentially expressed across developmental stages. Comparative genomic analysis identified 1458 C. macrocephalus specific genes, which were absent in I. punctatus. Gene network and protein-protein interaction analyses identified 26 key hub genes involved in the air-breathing function. Three top candidate genes, mb, ngb, hbae, are mainly associated with oxygen carrying, oxygen binding, and heme binding activities. Our study provides a rich data set for exploring the genomic basis of air-breathing function in C. macrocephalus and offers insights into the adaption to hypoxic environments.
Collapse
Affiliation(s)
- Xiaoli Ma
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
| | - Max Bangs
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
- Department of Biological Science, Florida State University, Tallahassee, FL, 32304, USA
| | - Veronica Alston
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
| | - Nathan J C Backenstose
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Rhoda Mae Simora
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
- College of Fisheries and Ocean Sciences, University of the Philippines Visayas, Miagao, 5023, Iloilo, Philippines
| | - Wenwen Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
| | - De Xing
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
| | - Shangjia Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
| | - Zhi Ye
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Anthony G Moss
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thuy-Yen Duong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, 94000, Vietnam
| | - Xu Wang
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA.
- Department of Pathobiology, Auburn University, Auburn, AL, 36849, USA.
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
- Alabama Agricultural Experiment Station, Auburn, AL, 36849, USA.
| |
Collapse
|