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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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Audira G, Siregar P, Chen KHC, Roldan MJM, Huang JC, Lai HT, Hsiao CD. Interspecies Behavioral Variability of Medaka Fish Assessed by Comparative Phenomics. Int J Mol Sci 2021; 22:ijms22115686. [PMID: 34073632 PMCID: PMC8197923 DOI: 10.3390/ijms22115686] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/23/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022] Open
Abstract
Recently, medaka has been used as a model organism in various research fields. However, even though it possesses several advantages over zebrafish, fewer studies were done in medaka compared to zebrafish, especially with regard to its behavior. Thus, to provide more information regarding its behavior and to demonstrate the behavioral differences between several species of medaka, we compared the behavioral performance and biomarker expression in the brain between four medaka fishes, Oryzias latipes, Oryzias dancena, Oryzias woworae, and Oryzias sinensis. We found that each medaka species explicitly exhibited different behaviors to each other, which might be related to the different basal levels of several biomarkers. Furthermore, by phenomics and genomic-based clustering, the differences between these medaka fishes were further investigated. Here, the phenomic-based clustering was based on the behavior results, while the genomic-based clustering was based on the sequence of the nd2 gene. As we expected, both clusterings showed some resemblances to each other in terms of the interspecies relationship between medaka and zebrafish. However, this similarity was not displayed by both clusterings in the medaka interspecies comparisons. Therefore, these results suggest a re-interpretation of several prior studies in comparative biology. We hope that these results contribute to the growing database of medaka fish phenotypes and provide one of the foundations for future phenomics studies of medaka fish.
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Affiliation(s)
- Gilbert Audira
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (G.A.); (P.S.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
| | - Petrus Siregar
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (G.A.); (P.S.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
| | - Kelvin H.-C. Chen
- Department of Applied Chemistry, National Pingtung University, Pingtung 900391, Taiwan;
| | - Marri Jmelou M. Roldan
- Faculty of Pharmacy and The Graduate School, University of Santo Tomas, Manila 1008, Philippines;
| | - Jong-Chin Huang
- Department of Applied Chemistry, National Pingtung University, Pingtung 900391, Taiwan;
- Correspondence: (J.-C.H.); (H.-T.L.); (C.-D.H.)
| | - Hong-Thih Lai
- Department of Aquatic Biosciences, National Chiayi University, 300 University Rd., Chiayi 600, Taiwan
- Correspondence: (J.-C.H.); (H.-T.L.); (C.-D.H.)
| | - Chung-Der Hsiao
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (G.A.); (P.S.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
- Research Center for Aquatic Toxicology and Pharmacology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
- Correspondence: (J.-C.H.); (H.-T.L.); (C.-D.H.)
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Pandey M, Kumar R, Srivastava P, Agarwal S, Srivastava S, Nagpure NS, Jena JK, Kushwaha B. WGSSAT: A High-Throughput Computational Pipeline for Mining and Annotation of SSR Markers From Whole Genomes. J Hered 2019; 109:339-343. [PMID: 28992259 DOI: 10.1093/jhered/esx075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022] Open
Abstract
Mining and characterization of Simple Sequence Repeat (SSR) markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. Whole genome sequencing (WGS)-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, noncoding RNA (ncRNA), core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic, and core gene region) along with primer identification and mining of cross-species markers. The program also generates a detailed statistical report along with visualization of mapped SSRs, genes, core genes, and RNAs. The features of WGSSAT were demonstrated using Takifugu rubripes data. This yielded a total of 139 057 SSR, out of which 113 703 SSR primer pairs were uniquely amplified in silico onto a T. rubripes (fugu) genome. Out of 113 703 mined SSRs, 81 463 were from coding region (including 4286 exonic and 77 177 intronic), 7 from RNA, 267 from core genes of fugu, whereas 105 641 SSR and 601 SSR primer pairs were uniquely mapped onto the medaka genome. WGSSAT is tested under Ubuntu Linux. The source code, documentation, user manual, example dataset and scripts are available online at https://sourceforge.net/projects/wgssat-nbfgr.
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Affiliation(s)
- Manmohan Pandey
- Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India.,AMITY Institute of Biotechnology, AMITY University, Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Ravindra Kumar
- Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Prachi Srivastava
- AMITY Institute of Biotechnology, AMITY University, Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Suyash Agarwal
- Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Shreya Srivastava
- Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Naresh S Nagpure
- Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Joy K Jena
- Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Basdeo Kushwaha
- Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
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XU W, CHEN S. Genomics and genetic breeding in aquatic animals: progress and prospects. FRONTIERS OF AGRICULTURAL SCIENCE AND ENGINEERING 2017; 4:305. [DOI: 10.15302/j-fase-2017154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Dohm JC, Lange C, Holtgräwe D, Sörensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H. Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:528-540. [PMID: 22211633 DOI: 10.1111/j.1365-313x.2011.04898.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.
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Affiliation(s)
- Juliane C Dohm
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
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Porazinski SR, Wang H, Furutani-Seiki M. Essential techniques for introducing medaka to a zebrafish laboratory--towards the combined use of medaka and zebrafish for further genetic dissection of the function of the vertebrate genome. Methods Mol Biol 2011; 770:211-241. [PMID: 21805266 DOI: 10.1007/978-1-61779-210-6_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The medaka, Oryzias latipes, a small egg-laying freshwater fish, is one of the three vertebrate model organisms in which genome-wide phenotype-driven mutant screens have been carried out. Despite a number of large-scale screens in zebrafish, a substantial number of mutants with new distinct phenotypes were identified in similar large-scale screens in the medaka. This observed difference in phenotype is due to the two species having a unique combination of genetic, biological and evolutional properties. The two genetic models share a whole-genome duplication event over that of tetrapods; however, each has independently specialized or lost the function of one of the two paralogues. The two fish species complement each other as genetic systems as straightforward comparison of phenotypes, ease of side-by-side analysis using the same techniques and simple and inexpensive husbandry of mutants make these small teleosts quite powerful in combination. Furthermore, both have draft genome sequences and bioinformatic tools available that facilitate further genetic dissection including whole-genome approaches. Together with the gene-driven approach to generate gene knockout mutants of the fish models, the two fish models complement the mouse in genetically dissecting vertebrate genome functions. The external embryogenesis and transparent embryos of the fish allow systematic isolation of embryonic lethal mutations, the most difficult targets in mammalian mutant screens. This chapter will describe how to work with both medaka and zebrafish almost as one species in a lab, focusing on medaka and highlighting the differences between the medaka and zebrafish systems.
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Affiliation(s)
- Sean R Porazinski
- Department of Biology and Biochemistry, Centre for Regenerative Medicine, The University of Bath, Bath, UK
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A Comparative BAC map for the gilthead sea bream (Sparus aurata L.). J Biomed Biotechnol 2010; 2011:329025. [PMID: 21049003 PMCID: PMC2964914 DOI: 10.1155/2011/329025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 09/10/2010] [Accepted: 09/23/2010] [Indexed: 12/18/2022] Open
Abstract
This study presents the first comparative BAC map of the gilthead sea bream (Sparus aurata), a highly valuated marine aquaculture fish species in the Mediterranean. High-throughput end sequencing of a BAC library yielded 92,468 reads (60.6 Mbp). Comparative mapping was achieved by anchoring BAC end sequences to the three-spined stickleback (Gasterosteus aculeatus) genome. BACs that were consistently ordered along the stickleback chromosomes accounted for 14,265 clones. A fraction of 5,249 BACs constituted a minimal tiling path that covers 73.5% of the stickleback chromosomes and 70.2% of the genes that have been annotated. The N50 size of 1,485 “BACtigs” consisting of redundant BACs is 337,253 bp. The largest BACtig covers 2.15 Mbp in the stickleback genome. According to the insert size distribution of mapped BACs the sea bream genome is 1.71-fold larger than the stickleback genome. These results represent a valuable tool to researchers in the field and may support future projects to elucidate the whole sea bream genome.
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Matsunaga W, Watanabe E. Habituation of medaka (Oryzias latipes) demonstrated by open-field testing. Behav Processes 2010; 85:142-50. [PMID: 20615458 DOI: 10.1016/j.beproc.2010.06.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 06/16/2010] [Accepted: 06/29/2010] [Indexed: 01/11/2023]
Abstract
Habituation to novel environments is frequently studied to analyze cognitive phenotypes in animals, and an open-field test is generally conducted to investigate the changes that occur in animals during habituation. The test has not been used in behavioral studies of medaka (Oryzias latipes), which is recently being used in behavioral research. Therefore, we examined the open-field behavior of medaka on the basis of temporal changes in 2 conventional indexes of locomotion and position. The findings of our study clearly showed that medaka changed its behavior through multiple temporal phases as it became more familiar with new surroundings; this finding is consistent with those of other ethological studies in animals. During repeated open-field testing on 2 consecutive days, we observed that horizontal locomotion on the second day was less than that on the first day, which suggested that habituation is retained in fish for days. This temporal habituation was critically affected by water factors or visual cues of the tank, thereby suggesting that fish have spatial memory of their surroundings. Thus, the data from this study will afford useful fundamental information for behavioral phenotyping of medaka and for elucidating cognitive phenotypes in animals.
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Affiliation(s)
- Wataru Matsunaga
- Laboratory of Neurophysiology, National Institute for Basic Biology, Higashiyama 5-1, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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Kuhl H, Beck A, Wozniak G, Canario AVM, Volckaert FAM, Reinhardt R. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics 2010; 11:68. [PMID: 20105308 PMCID: PMC2837037 DOI: 10.1186/1471-2164-11-68] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 01/27/2010] [Indexed: 11/20/2022] Open
Abstract
Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.
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Affiliation(s)
- Heiner Kuhl
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany.
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Iwanami N, Okada M, Hoa VQ, Seo Y, Mitani H, Sasaki T, Shimizu N, Kondoh H, Furutani-Seiki M, Takahama Y. Ethylnitrosourea-induced thymus-defective mutants identify roles of KIAA1440, TRRAP, and SKIV2L2 in teleost organ development. Eur J Immunol 2009; 39:2606-16. [PMID: 19670383 DOI: 10.1002/eji.200939362] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The thymus is an organ where T lymphocytes develop. Thymus development requires interactions of cells derived from three germ layers. However, the molecular mechanisms that control thymus development are not fully understood. To identify the genes that regulate thymus development, we previously carried out a large-scale screening for ethylnitrosourea-induced mutagenesis using medaka, Oryzias latipes, and established a panel of recessive thymus-lacking mutants. Here we report the identification of three genes responsible for these mutations. We found that the mutations in KIAA1440, TRRAP, and SKIV2L2 caused the defects in distinct steps of thymus development. We also found that these genes were widely expressed in many organs and that the mutations in these genes caused defects in the development of various other organs. These results enabled us to identify previously unknown roles of widely expressed genes in medaka organ development. The possible reasons why thymus-defective teleost mutants could be used to identify widely expressed genes and future strategies to increase the likelihood of identifying genes that specifically regulate thymus development are discussed.
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Affiliation(s)
- Norimasa Iwanami
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan.
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Martinez-Morales JR, Rembold M, Greger K, Simpson JC, Brown KE, Quiring R, Pepperkok R, Martin-Bermudo MD, Himmelbauer H, Wittbrodt J. ojoplano-mediated basal constriction is essential for optic cup morphogenesis. Development 2009; 136:2165-75. [DOI: 10.1242/dev.033563] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although the vertebrate retina is a well-studied paradigm for organogenesis, the morphogenetic mechanisms that carve the architecture of the vertebrate optic cup remain largely unknown. Understanding how the hemispheric shape of an eye is formed requires addressing the fundamental problem of how individual cell behaviour is coordinated to direct epithelial morphogenesis. Here, we analyze the role of ojoplano (opo), an uncharacterized gene whose human ortholog is associated with orofacial clefting syndrome, in the morphogenesis of epithelial tissues. Most notably,when opo is mutated in medaka fish, optic cup folding is impaired. We characterize optic cup morphogenesis in vivo and determine at the cellular level how opo affects this process. opo encodes a developmentally regulated transmembrane protein that localizes to compartments of the secretory pathway and to basal end-feet of the neuroepithelial precursors. We show that Opo regulates the polarized localization of focal adhesion components to the basal cell surface. Furthermore, tissue-specific interference with integrin-adhesive function impairs optic cup folding,resembling the ocular phenotype observed in opo mutants. We propose a model of retinal morphogenesis whereby opo-mediated formation of focal contacts is required to transmit the mechanical tensions that drive the macroscopic folding of the vertebrate optic cup.
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Affiliation(s)
- Juan Ramon Martinez-Morales
- Developmental unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Centro Andaluz de Biología del Desarrollo (UPO/CSIC), 41013 Sevilla,Spain
| | - Martina Rembold
- Developmental unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Klaus Greger
- Cell Biology unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jeremy C. Simpson
- Cell Biology unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Rebecca Quiring
- Developmental unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rainer Pepperkok
- Cell Biology unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Heinz Himmelbauer
- Max-Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin-Dahlem, Germany
| | - Joachim Wittbrodt
- Developmental unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Iwanami N, Higuchi T, Sasano Y, Fujiwara T, Hoa VQ, Okada M, Talukder SR, Kunimatsu S, Li J, Saito F, Bhattacharya C, Matin A, Sasaki T, Shimizu N, Mitani H, Himmelbauer H, Momoi A, Kondoh H, Furutani-Seiki M, Takahama Y. WDR55 is a nucleolar modulator of ribosomal RNA synthesis, cell cycle progression, and teleost organ development. PLoS Genet 2008; 4:e1000171. [PMID: 18769712 PMCID: PMC2515640 DOI: 10.1371/journal.pgen.1000171] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 07/17/2008] [Indexed: 01/07/2023] Open
Abstract
The thymus is a vertebrate-specific organ where T lymphocytes are generated. Genetic programs that lead to thymus development are incompletely understood. We previously screened ethylnitrosourea-induced medaka mutants for recessive defects in thymus development. Here we report that one of those mutants is caused by a missense mutation in a gene encoding the previously uncharacterized protein WDR55 carrying the tryptophan-aspartate-repeat motif. We find that WDR55 is a novel nucleolar protein involved in the production of ribosomal RNA (rRNA). Defects in WDR55 cause aberrant accumulation of rRNA intermediates and cell cycle arrest. A mutation in WDR55 in zebrafish also leads to analogous defects in thymus development, whereas WDR55-null mice are lethal before implantation. These results indicate that WDR55 is a nuclear modulator of rRNA synthesis, cell cycle progression, and embryonic organogenesis including teleost thymus development.
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Affiliation(s)
- Norimasa Iwanami
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Tomokazu Higuchi
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Yumi Sasano
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Toshinobu Fujiwara
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Vu Q. Hoa
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Minoru Okada
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Sadiqur R. Talukder
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Sanae Kunimatsu
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Jie Li
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Fumi Saito
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
| | - Chitralekha Bhattacharya
- Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Angabin Matin
- Department of Cancer Genetics, University of Texas, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Takashi Sasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
- GSP Center, The Leading Institute of Keio University, Tsukuba, Japan
| | - Nobuyoshi Shimizu
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
- GSP Center, The Leading Institute of Keio University, Tsukuba, Japan
| | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | | | - Akihiro Momoi
- Developmental Mutants Group, Kondoh Differentiation Signaling Project, Japan Science and Technology Agency, Kyoto, Japan
| | - Hisato Kondoh
- Developmental Mutants Group, Kondoh Differentiation Signaling Project, Japan Science and Technology Agency, Kyoto, Japan
| | - Makoto Furutani-Seiki
- Developmental Mutants Group, Kondoh Differentiation Signaling Project, Japan Science and Technology Agency, Kyoto, Japan
| | - Yousuke Takahama
- Division of Experimental Immunology, Institute for Genome Research, University of Tokushima, Tokushima, Japan
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13
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Selected papers on zebrafish and other aquarium fish models. Zebrafish 2008; 1:165-72. [PMID: 18248227 DOI: 10.1089/zeb.2004.1.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Terzibasi E, Valenzano DR, Cellerino A. The short-lived fish Nothobranchius furzeri as a new model system for aging studies. Exp Gerontol 2007; 42:81-9. [PMID: 17049789 DOI: 10.1016/j.exger.2006.06.039] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 06/02/2006] [Accepted: 06/07/2006] [Indexed: 12/17/2022]
Abstract
Genetic and pharmacological research on aging is hampered by the lifespan of available vertebrate models. We recently initiated studies on Nothobranchius furzeri, a species with a maximum life expectancy in captivity of just three months which represents the shortest documented captive lifespan for a vertebrate. Further research on N. furzeri has demonstrated that 1. Short lifespan is tied with explosive growth and accelerated sexual maturation. 2. Short lifespan is correlated with expression of age-related behavioral and histological changes. 3. Lifespan and expression of age-related markers can be modulated by water temperature. 4. Resveratrol, a drug characterized for its life-extending action in Caenorhabditis elegans and Drosophila, increases lifespan and retards expression of age-related markers. 5. Aging-related genes can be easily isolated by homology cloning. Finally, different populations or species of Nothobranchius show large-scale differences in captive lifespan. In the last three years, N. furzeri has moved from biological curiosity to a promising model system for drug validation. Furthermore, this species occupies a favorable position in the Teleost's "tree of life". It is very close to the Japanese Medaka, and close to the pufferfishes and stickleback and might represent a very useful model for comparative genomics of aging.
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15
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Sasaki T, Shimizu A, Ishikawa SK, Imai S, Asakawa S, Murayama Y, Khorasani MZ, Mitani H, Furutani-Seiki M, Kondoh H, Nanda I, Schmid M, Schartl M, Nonaka M, Takeda H, Hori H, Himmelbauer H, Shima A, Shimizu N. The DNA sequence of medaka chromosome LG22. Genomics 2007; 89:124-33. [PMID: 17067776 DOI: 10.1016/j.ygeno.2006.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 08/31/2006] [Accepted: 09/09/2006] [Indexed: 10/24/2022]
Abstract
We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka (Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the "conserved gene cluster" (CGC), a strict definition of "synteny" at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520-23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage.
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Affiliation(s)
- Takashi Sasaki
- Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Tokyo 160-8582, Japan
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16
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Abstract
The last common ancestor between fish and mammals dates back to the very origin of the vertebrate lineage and today, half of modern vertebrates are fish. It is thus not surprising that several fish species have played important roles in recent years to advance our understanding of vertebrate genome evolution, to inform us on the structure of human genes, and, somewhat more unexpectedly, to provide leads to understanding the function of genes involved in human diseases. Genome sequence comparisons between such distantly related organisms are highly informative due to the accumulation of neutral mutations in nonfunctional regions. Yet humans and fishes share many developmental pathways, organ systems, and physiological mechanisms, making conclusions relevant to human biology. The respective advantages of zebrafish, medaka, Tetraodon, or Takifugu have been well exploited so far with bioinformatics analyses and molecular biology techniques. However the full potential of fish genomics is about to be unleashed with the integration of more traditional disciplines such as biochemistry and physiology, with the study of additional species such as carp, trout, or tilapia and a broadening of its applications to environmental genomics or aquaculture.
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Affiliation(s)
- Hugues Roest Crollius
- Dyogen Lab, Centre National de la Recherche Scientifique UMR8541, Ecole Normale Supérieure, 75005 Paris, France.
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17
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Shimizu N, Sasaki T, Asakawa S, Shimizu A, Ishikawa SK, Imai S, Murayama Y, Himmelbauer H, Mitani H, Furutani-Seiki M, Kondoh H, Schartl M, Nonaka M, Takeda H, Hori H, Shima A. Comparative genomics of medaka and fugu. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2006; 1:6-12. [PMID: 20483229 DOI: 10.1016/j.cbd.2005.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2005] [Revised: 10/19/2005] [Accepted: 10/19/2005] [Indexed: 11/20/2022]
Abstract
A small freshwater fish medaka (Oryzias latipes) has been one of the most attractive experimental systems for research in genetics and developmental biology. We have formed an international consortium Medaka Genome Initiative (MGI) to collect and share various information and resources on medaka. The MGI has set an ambitious goal aiming at the complete sequencing of the medaka genome and as a feasibility study we have begun sequencing one particular chromosome, linkage group 22 (LG22) of approximately 22 Mb in size. Initial sequence analysis revealed unique features of the medaka genome in comparison to fugu genome.
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18
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Fischer U, Utke K, Somamoto T, Köllner B, Ototake M, Nakanishi T. Cytotoxic activities of fish leucocytes. FISH & SHELLFISH IMMUNOLOGY 2006; 20:209-26. [PMID: 15939625 DOI: 10.1016/j.fsi.2005.03.013] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Revised: 03/03/2005] [Accepted: 03/03/2005] [Indexed: 05/02/2023]
Abstract
Like mammalian leucocytes, white blood cells of fish are able to kill altered (e.g. virus-infected) and foreign (allogeneic or xenogeneic) cells. The existence of natural killer (NK)-like and specific cytotoxic cells in fish was first shown using allogeneic and xenogeneic effector/target cell systems. In addition to in vivo and ex vivo studies, very important contributions were made by in vitro analysis using a number of different long-term cytotoxic cell lines established from channel catfish. In mammals, specific cell-mediated cytotoxicity (CMC) as part of the adaptive immune response requires a number of key molecules expressed on effector leucocytes and target cells. CD8+ T lymphocytes kill infected cells only, if their antigen receptor (TCR) matches the MHC class I with bound peptide of the target cell. Expression patterns of the fish gene homologues for TCR, CD8 and MHC class I, as well as related genes, are in agreement with similar function. Convenient systems for the analysis of specific CMC have only recently become available for fish with the combination of clonal fish with syngeneic or allogeneic but MHC class I matching cell lines. It was demonstrated that both, NK- and cytotoxic T (Tc) cells are involved in the killing of virus infected MHC class I matching and mismatching target cells. Analysis of these lymphocyte subsets is only starting for fish. There is also evidence that the different viral proteins trigger different subsets of killer cells. This review further discusses findings on fish CMC with regard to temperature/seasons and ontogeny.
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Affiliation(s)
- Uwe Fischer
- Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, D-17493 Greifswald-Insel Riems, Germany.
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19
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Abstract
Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.
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Affiliation(s)
- J-N Volff
- BioFuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, am Hubland, D-97074 Würzburg, Germany.
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20
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Furutani-Seiki M, Sasado T, Morinaga C, Suwa H, Niwa K, Yoda H, Deguchi T, Hirose Y, Yasuoka A, Henrich T, Watanabe T, Iwanami N, Kitagawa D, Saito K, Asaka S, Osakada M, Kunimatsu S, Momoi A, Elmasri H, Winkler C, Ramialison M, Loosli F, Quiring R, Carl M, Grabher C, Winkler S, Del Bene F, Shinomiya A, Kota Y, Yamanaka T, Okamoto Y, Takahashi K, Todo T, Abe K, Takahama Y, Tanaka M, Mitani H, Katada T, Nishina H, Nakajima N, Wittbrodt J, Kondoh H. A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes. Mech Dev 2005; 121:647-58. [PMID: 15210174 DOI: 10.1016/j.mod.2004.04.016] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2004] [Revised: 03/22/2004] [Accepted: 04/21/2004] [Indexed: 01/24/2023]
Abstract
A large-scale mutagenesis screen was performed in Medaka to identify genes acting in diverse developmental processes. Mutations were identified in homozygous F3 progeny derived from ENU-treated founder males. In addition to the morphological inspection of live embryos, other approaches were used to detect abnormalities in organogenesis and in specific cellular processes, including germ cell migration, nerve tract formation, sensory organ differentiation and DNA repair. Among 2031 embryonic lethal mutations identified, 312 causing defects in organogenesis were selected for further analyses. From these, 126 mutations were characterized genetically and assigned to 105 genes. The similarity of the development of Medaka and zebrafish facilitated the comparison of mutant phenotypes, which indicated that many mutations in Medaka cause unique phenotypes so far unrecorded in zebrafish. Even when mutations of the two fish species cause a similar phenotype such as one-eyed-pinhead or parachute, more genes were found in Medaka than in zebrafish that produced the same phenotype when mutated. These observations suggest that many Medaka mutants represent new genes and, therefore, are important complements to the collection of zebrafish mutants that have proven so valuable for exploring genomic function in development.
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Affiliation(s)
- Makoto Furutani-Seiki
- Japan Science and Technology Corporation, Kondoh Differentiation Signaling Project, Kawaaracho 14, Yoshida, Sakyoku, Kyoto 606-8305, Japan.
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21
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Nguyen G, Bukanov N, Oshimura M, Smith CL. Cloneless genomic DNA analysis: an efficient and simple methods for de novo genomic sequencing projects and gap filling. ACTA ACUST UNITED AC 2005; 21:135-44. [PMID: 15748687 DOI: 10.1016/j.bioeng.2004.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2004] [Accepted: 08/19/2004] [Indexed: 11/23/2022]
Abstract
The utility of using genomic DNA directly in agarose, i.e. cloneless libraries, in place of large clone libraries, radiation hybrid panels, or chromosome dissection was demonstrated. The advantage of the cloneless library approach is that, in principle, a targeted genomic resource can be developed rapidly for any genomic region using any genomic DNA sample. Here, a human chromosome 20 Not I fragment library was generated by slicing a pulsed field gel lane containing fractionating Not I cleaved DNA from a monosomic hybrid cell line into 2 mm pieces. A reliable PCR method using agarose embedded DNA was developed. InterAlu PCR generated unique patterns of products from adjacent slices (e.g. fractions). Further, the specificity of the interAlu products was demonstrated by FISH analysis and in other hybridization experiments to arrayed interAlu products. STS content mapping was used to order the fractions and also demonstrate the unique content of the library fractions.
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Affiliation(s)
- Giang Nguyen
- Molecular Biotechnology Research Laboratory, Department of Biomedical Engineering, 36 Cummington Street, Boston, MA 02215, USA
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22
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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23
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Naruse K, Hori H, Shimizu N, Kohara Y, Takeda H. Medaka genomics: a bridge between mutant phenotype and gene function. Mech Dev 2004; 121:619-28. [PMID: 15210171 DOI: 10.1016/j.mod.2004.04.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 03/05/2004] [Accepted: 05/14/2004] [Indexed: 11/17/2022]
Abstract
Recent advances in medaka genetics have proven that the medakafish is an excellent model system for developmental and evolutionary biology studies and that it can complement similar studies in zebrafish. Large-scale mutagenesis projects are now being conducted by several groups in Japan and are delivering a vastly expanded pool of medaka mutant stocks. This growing availability of genomic resources will greatly accelerate progress in moving from mutant phenotypes to the elucidation of gene function. This phenotype-driven approach can be expected to lead to the identification and characterization of novel genes and pathways in vertebrate genomes. This review discusses the current state of medaka genomic resources, the state of medaka gene mapping and medaka genome sequencing projects.
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Affiliation(s)
- Kiyoshi Naruse
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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24
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Schartl M, Nanda I, Kondo M, Schmid M, Asakawa S, Sasaki T, Shimizu N, Henrich T, Wittbrodt J, Furutani-Seiki M, Kondoh H, Himmelbauer H, Hong Y, Koga A, Nonaka M, Mitani H, Shima A. Current status of medaka genetics and genomics. The Medaka Genome Initiative (MGI). Methods Cell Biol 2004; 77:173-99. [PMID: 15602912 DOI: 10.1016/s0091-679x(04)77010-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Manfred Schartl
- Biocenter, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
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