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Sarropoulou E, Fernandes JMO. Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 6:92-102. [PMID: 20961822 DOI: 10.1016/j.cbd.2010.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 12/14/2022]
Abstract
Comparative genomics is a powerful tool to transfer knowledge coming from model fish species to non-model fish species of economic or/and evolutionary interest. Such transfer is of importance as functional studies either are difficult to perform with most non-model species. The first comparative map constructed using the human and the chimpanzee genome allowed the identification of putative orthologues. Although comparative mapping in teleosts is still in its infancy, five model teleost genomes from different orders have been fully sequenced to date and the sequencing of several commercially important species are also underway or near completion. The accessibility of these whole genome sequences and rapid developments in genomics of fish species are paving the way towards new and valuable research in comparative genetics and genomics. With the accumulation of information in model species, the genetic and genomic characterization of non-model, but economically, physiologically or evolutionary important species is now feasible. Furthermore, comparison of low coverage gene maps of non-model fish species against fully sequenced fish species will enhance the efficiency of candidate gene identification projected for quantitative trait loci (QTL) scans for traits of special interest.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, Crete, Greece.
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Liu Z. Development of genomic resources in support of sequencing, assembly, and annotation of the catfish genome. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 6:11-7. [PMID: 20430707 DOI: 10.1016/j.cbd.2010.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 12/11/2022]
Abstract
Major progress has been made in catfish genomics including construction of high-density genetic linkage maps, BAC-based physical maps, and integration of genetic linkage and physical maps. Large numbers of ESTs have been generated from both channel catfish and blue catfish. Microarray platforms have been developed for the analysis of genome expression. Genome repeat structures are studied, laying grounds for whole genome sequencing. USDA recently approved funding of the whole genome sequencing project of catfish using the next generation sequencing technologies. Generation of the whole genome sequence is a historical landmark of catfish research as it opens the real first step of the long march toward genetic enhancement. The research community needs to be focused on aquaculture performance and production traits, take advantage of the unprecedented genome information and technology, and make real progress toward genetic improvements of aquaculture brood stocks.
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Affiliation(s)
- Zhanjiang Liu
- Department of Fisheries and Allied Aquacultures, Auburn University, AL 36849, USA.
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Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small BC, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, Liu Z. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol 2010; 11:R8. [PMID: 20096101 PMCID: PMC2847720 DOI: 10.1186/gb-2010-11-1-r8] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/14/2010] [Accepted: 01/22/2010] [Indexed: 12/13/2022] Open
Abstract
Twelve cDNA libraries from two species of catfish have been sequenced, resulting in the generation of nearly 500,000 ESTs. Background Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.
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Affiliation(s)
- Shaolin Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, 203 Swingle Hall, Auburn University, Auburn, AL 36849, USA.
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Yue GH, Zhu ZY, Wang CM, Xia JH. A simple and efficient method for isolating polymorphic microsatellites from cDNA. BMC Genomics 2009; 10:125. [PMID: 19320968 PMCID: PMC2667190 DOI: 10.1186/1471-2164-10-125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 03/25/2009] [Indexed: 11/21/2022] Open
Abstract
Background Microsatellites in cDNA are useful as molecular markers because they represent transcribed genes and can be used as anchor markers for linkage and comparative mapping, as well as for studying genome evolution. Microsatellites in cDNA can be detected in existing ESTs by data mining. However, in most fish species, no ESTs are available or the number of ESTs is limited, although fishes represent half of the vertebrates on the earth. We developed a simple and efficient method for isolation of microsatellites from cDNA in fish. Results The method included normalization of 150 ng cDNA using 0.5 U duplex-specific nuclease (DSN) at 65°C for 30 min, enrichment of microsatellites using biotinylated oligonucleotides and magnetic field, and directional cloning of cDNA into a vector. We tested this method to enrich CA- and GA-microsatellites from cDNA of Asian seabass, and demonstrated that enrichment of microsatellites from normalized cDNA could increased the efficiency of microsatellite isolation over 30 times as compared to direct sequencing of clones from cDNA libraries. One hundred and thirty-nine (36.2%) out of 384 clones from normalized cDNA contained microsatellites. Unique microsatellite sequences accounted for 23.6% (91/384) of sequenced clones. Sixty microsatellites isolated from cDNA were characterized, and 41 were polymorphic. The average allele number of the 41 microsatellites was 4.85 ± 0.54, while the expected heterozygosity was 0.56 ± 0.03. All the isolated microsatellites inherited in a Mendelian pattern. Conclusion Normalization of cDNA substantially increased the efficiency of enrichment of microsatellites from cDNA. The described method for isolation of microsatellites from cDNA has the potential to be applied to a wide range of fish species. The microsatellites isolated from cDNA could be useful for linkage and comparative mapping, as well as for studying genome evolution.
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Affiliation(s)
- Gen Hua Yue
- Molecular Population Genetics Group, Temasek Life Sciences Lab, 1 Research Link, National University of Singapore, 117604 Singapore.
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Wang S, Xu P, Thorsen J, Zhu B, de Jong PJ, Waldbieser G, Kucuktas H, Liu Z. Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2007; 9:701-11. [PMID: 17671813 DOI: 10.1007/s10126-007-9021-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 04/17/2007] [Accepted: 04/19/2007] [Indexed: 05/16/2023]
Abstract
The CHORI-212 bacterial artificial chromosome (BAC) library was constructed by cloning EcoRI/EcoRI partially digested DNA into the pTARBAC2.1 vector. The library has an average insert size of 161 kb, and provides 10.6-fold coverage of the channel catfish haploid genome. Screening of 32 genes using overgo or cDNA probes indicated that this library had a good representation of the genome as all tested genes existed in the library. We previously reported sequencing of approximately 25,000 BAC ends that generated 20,366 high-quality BAC end sequences (BES) and identified a large number of sequences similar to known genes using BLASTX searches. In this work, particular attention was given to identification of BAC mate pairs with known genes from both ends. When identified, comparative genome analysis was conducted to determine syntenic regions of the catfish genome with the genomes of zebrafish and Tetraodon. Of the 141 mate pairs with known genes from channel catfish, conserved syntenies were identified in 34 (24.1%), with 30 conserved in the zebrafish genome and 14 conserved in the Tetraodon genome. Additional analysis of three of the 34 conserved syntenic groups by direct sequencing indicated conserved gene contents in all three species. This indicates that comparative genome analysis may provide shortcuts to genome analysis in catfish, especially for short genomic regions once the conserved syntenies are identified.
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Affiliation(s)
- Shaolin Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA
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CHEN SL, MA HY, JIANG Y, LIAO XL, MENG L. Isolation and characterization of polymorphic microsatellite loci from an EST library of turbot (Scophthalmus maximus) and cross-species amplification. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01725.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Although there are differences in performance between genetic groups of channel catfish, identification and management of these groups is difficult because catfish strains look alike and individuals cannot be tagged efficiently. Thus, US catfish producers have not been able to objectively identify fish from different strains or populations, and it has been difficult for them to maintain the genetic purity of populations on the farm. We have developed a multiplexed microsatellite genotyping system to define catfish populations based on allelic frequency and exclusion. A commercial catfish genotype database was developed using catfish samples collected from 24 processing plants in the four main US catfish-producing states. The utility of the system was tested by the molecular characterization of the USDA103 research strain. Using eight microsatellite loci, the probability of falsely classifying an individual non-USDA103 catfish as a USDA103 was 0.0065. From a sample of 50 fish from a putative USDA103 pond, the probability of falsely including two non-USDA103 fish was 1 x 10(-105), and the conservative probability of falsely excluding two USDA103 fish was 1 x 10(-6). This genotyping system provides channel catfish producers with an objective mechanism for identification and management of genetically selected fish.
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Affiliation(s)
- G C Waldbieser
- USDA, Agricultural Research Service, Catfish Genetics Research Unit, 141 Experiment Station Road, Stoneville, MS, USA.
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Quiniou SMA, Waldbieser GC, Duke MV. A first generation BAC-based physical map of the channel catfish genome. BMC Genomics 2007; 8:40. [PMID: 17284319 PMCID: PMC1800894 DOI: 10.1186/1471-2164-8-40] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Accepted: 02/06/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Channel catfish, Ictalurus punctatus, is the leading species in North American aquaculture. Genetic improvement of catfish is performed through selective breeding, and genomic tools will help improve selection efficiency. A physical map is needed to integrate the genetic map with the karyotype and to support fine mapping of phenotypic trait alleles such as Quantitative Trait Loci (QTL) and the effective positional cloning of genes. RESULTS A genome-wide physical map of the channel catfish was constructed by High-Information-Content Fingerprinting (HICF) of 46,548 Bacterial Artificial Chromosomes (BAC) clones using the SNaPshot technique. The clones were assembled into contigs with FPC software. The resulting assembly contained 1,782 contigs and covered an estimated physical length of 0.93 Gb. The validity of the assembly was demonstrated by 1) anchoring 19 of the largest contigs to the microsatellite linkage map 2) comparing the assembly of a multi-gene family to Restriction Fragment Length Polymorphism (RFLP) patterns seen in Southern blots, and 3) contig sequencing. CONCLUSION This is the first physical map for channel catfish. The HICF technique allowed the project to be finished with a limited amount of human resource in a high throughput manner. This physical map will greatly facilitate the detailed study of many different genomic regions in channel catfish, and the positional cloning of genes controlling economically important production traits.
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Affiliation(s)
| | | | - Mary V Duke
- USDA-ARS/CGRU, 141 Experiment Station Rd, Stoneville, MS 38776, USA
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Karsi A, Wolters WR, Waldbieser GC. Assignment of immune-related genes to the channel catfish, Ictalurus punctatus, genetic map. Anim Genet 2006; 36:502-6. [PMID: 16293124 DOI: 10.1111/j.1365-2052.2005.01345.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eighteen new genes, adenosine A1 receptor (ADORA1), complement component 4-beta (C4b), complement component 8-beta (C8b), chemokine ligand 19 (CCL19), chemokine ligand 21 (CCL21), chemokine ligand 25 (CCL25), chemokine receptor 2 (CCR2), chemokine receptor 5 (CCR5), chemokine receptor 4 (CCR4), chemokine receptor 7 (CCR7), chemokine receptor 9 (CCR9), interleukin 1-beta (IL1B), integrin II-beta (ITGB2), novel immune type receptor 2 (NITR2), novel immune type receptor 4 (NITR4), natural killer cell lysin (NKLYSIN), nucleotide excision repair (RAD23B) and tumour necrosis factor-alpha (TNF), were assigned to the channel catfish (Ictalurus punctatus) genetic linkage map. Polymorphic microsatellite markers were developed for NITR2, NITR4 and RAD23B from short-tandem repeats in the available sequence. Polymorphic microsatellite markers were developed for the remaining 15 genes by short-tandem repeat-anchored primer sequencing of catfish bacterial artificial chromosomes. Two gene clusters (MYOG-NRAMP-ADORA1) and (CCR4-CCR2-CCR5) displayed conservation of synteny between catfish and mammals. Assignment of 18 new genes to the catfish linkage map will further advance integration of genetic and physical maps and comparative mapping between channel catfish and map rich species.
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Affiliation(s)
- A Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, PO Box 6100, Mississippi State, MS 39762-6100, USA
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Li RW, Waldbieser GC. Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus. BMC Genomics 2006; 7:134. [PMID: 16740160 PMCID: PMC1501020 DOI: 10.1186/1471-2164-7-134] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 06/01/2006] [Indexed: 11/20/2022] Open
Abstract
Background Functional analysis of the catfish genome will be useful for the identification of genes controlling traits of economic importance, especially innate disease resistance. However, this species lacks a platform for global gene expression profiling, so we designed a first generation high-density oligonucleotide microarray platform based on channel catfish EST sequences. This platform was used to profile gene expression in catfish spleens 2 h, 4 h, 8 h and 24 h after injection of lipopolysaccharide (LPS). Results In the spleen samples, 138 genes were significantly induced or repressed greater than 2-fold by LPS treatment. Real-time RT-PCR was used to verify the microarray results for nine selected genes representing different expression levels. The results from real-time RT-PCR were positively correlated (R2 = 0.87) with the results from the microarray. Conclusion The first generation channel catfish microarray provided several candidate genes useful for further evaluation of immune response mechanisms in this species. This research will help us to better understand recognition of LPS by host cells and the LPS-signalling pathway in fish.
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Affiliation(s)
- Robert W Li
- USDA, Agricultural Research Service, Catfish Genetics Research Unit, Stoneville, MS 38776, USA
- USDA, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA
| | - Geoffrey C Waldbieser
- USDA, Agricultural Research Service, Catfish Genetics Research Unit, Stoneville, MS 38776, USA
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