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Zhang Y, Xia H, Peng W, Liu L, Liu L, Yang P. Application of Repetitive Sequences in Fish Cell Depletion as a Target for the CRISPR/Cas9 System. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10328-6. [PMID: 38833200 DOI: 10.1007/s10126-024-10328-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/27/2024] [Indexed: 06/06/2024]
Abstract
Specific cell depletion is a common means to study the physiological function of cell lineages and tissue regeneration. However, 100% depletion is difficult to achieve with existing cell depletion strategies. With the increasing maturity of CRISPR/Cas9 technology, it is increasingly used for the depletion of various cells. However, even with this technology, it is difficult to complete the depletion of specific gene knockout cells. For this reason, cell depletion with the use of repetitive sequences as the target of CRISPR/Cas9 was explored using zebrafish. All cells were used as the target cells for the first set of experiments. The results showed that injection of a mixture of DANA-gRNA and Cas9 mRNA into zygotes resulted in substantial cell apoptosis. Cells are almost invisible in the embryonic animal pole during the dome stage. The activities of the caspase-3 and caspase-9 proteins and the mRNA level of the P53 gene were significantly increased. Then, primordial germ cells (PGCs) in embryos were used as the target cells in subsequent experiments. To specifically knock out PGCs, we injected the mix of DANA-gRNA, pkop: Cas9 plasmid (the kop promotor allows Cas9 expression only in PGCs), and eGFP-nos3'UTR mRNA into zebrafish fertilized eggs. The results revealed that the activity of the caspase-3 protein was significantly increased, and the mRNA levels of P53, ku70, and ku80 were significantly upregulated, while the number of PGCs decreased gradually. Few PGCs labeled with GFP could be seen 20 h post-fertilization (hpf), and no PGCs could be seen at the germinal ridge 24 hpf. Therefore, the combination of CRISPR/Cas9 technology and repetitive sequences can achieve efficient cell depletion regardless of whether there is generalized expression or expression in specific cells. These results indicate that it is feasible to eliminate cells by using repeat sequences as CRISPR/Cas9 system target sites.
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Affiliation(s)
- Yunsheng Zhang
- Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Engineering Research Center of Aquatic Organism Resources and Environmental Ecology, Zoology Key Laboratory of Hunan Higher Education, Changde Research Center for Agricultural Biomacromolecule, Innovation Team of Microbial Technology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China.
| | - Hu Xia
- Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Engineering Research Center of Aquatic Organism Resources and Environmental Ecology, Zoology Key Laboratory of Hunan Higher Education, Changde Research Center for Agricultural Biomacromolecule, Innovation Team of Microbial Technology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Wei Peng
- Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Engineering Research Center of Aquatic Organism Resources and Environmental Ecology, Zoology Key Laboratory of Hunan Higher Education, Changde Research Center for Agricultural Biomacromolecule, Innovation Team of Microbial Technology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Lanhai Liu
- Changde Fishery Administration Station, Changde, China
| | - Liangguo Liu
- Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Engineering Research Center of Aquatic Organism Resources and Environmental Ecology, Zoology Key Laboratory of Hunan Higher Education, Changde Research Center for Agricultural Biomacromolecule, Innovation Team of Microbial Technology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
| | - Pinhong Yang
- Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Engineering Research Center of Aquatic Organism Resources and Environmental Ecology, Zoology Key Laboratory of Hunan Higher Education, Changde Research Center for Agricultural Biomacromolecule, Innovation Team of Microbial Technology, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, China
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2
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Curzon AY, Dor L, Shirak A, Meiri-Ashkenazi I, Rosenfeld H, Ron M, Seroussi E. A novel c.1759T>G variant in follicle-stimulating hormone-receptor gene is concordant with male determination in the flathead grey mullet (Mugil cephalus). G3-GENES GENOMES GENETICS 2021; 11:6046932. [PMID: 33589926 PMCID: PMC8022982 DOI: 10.1093/g3journal/jkaa044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Various master key regulators (MKRs) that control a binary switch of sex determination (SD) have been found in fish; these provide an excellent model for the study of vertebrate genetic SD. The SD region in flathead grey mullet has been previously mapped to a 1 Mbp region harboring 27 genes, of which one is follicle-stimulating hormone receptor (fshr). Although this gene is involved in gonad differentiation and function, it has not been considered as an MKR of SD. We systematically investigated polymorphism in mullet fshr using DNA shotgun sequences, and compared them between males and females. Capable of encoding nonconservative amino acid substitutions, c.1732G>A and c.1759T>G exhibited association with sex on a population level (N = 83; P ≤ 6.7 × 10-19). Hence, 1732 A and 1759 G represent a male-specific haplotype of the gene, designated as "fshry." Additional flanking SNPs showed a weaker degree of association with sex, delimiting the SD critical region to 143 nucleotides on exon 14. Lack of homozygotes for fshry, and the resulting divergence from Hardy-Weinberg equilibrium (N = 170; P ≤ 3.9 × 10-5), were compatible with a male heterogametic model (XY/XX). Capable of replacing a phenylalanine with valine, c.1759T>G alters a conserved position across the sixth transmembrane domain of vertebrate FSHRs. Amino acid substitutions in this position in vertebrates are frequently associated with constant receptor activation and consequently with FSH/FSHR signaling alteration; thus, indicating a potential role of fshr as an MKR of SD.
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Affiliation(s)
- Arie Y Curzon
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel.,Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Lior Dor
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel.,Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
| | - Iris Meiri-Ashkenazi
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Hana Rosenfeld
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Micha Ron
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
| | - Eyal Seroussi
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
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3
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Kratochwil CF, Liang Y, Urban S, Torres-Dowdall J, Meyer A. Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Cichlid Fishes. Genome Biol Evol 2019; 11:3452-3465. [PMID: 31821504 PMCID: PMC6916709 DOI: 10.1093/gbe/evz261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8-12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
- Zukunftskolleg, University of Konstanz, Germany
| | - Yipeng Liang
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
| | - Sabine Urban
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Julián Torres-Dowdall
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- Zukunftskolleg, University of Konstanz, Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Germany
- International Max Planck Research School for Organismal Biology (IMPRS), Max Planck Institute for Ornithology, Radolfzell, Germany
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4
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Mapping of the Sex Determining Region on Linkage Group 12 of Guppy ( Poecilia reticulata). G3-GENES GENOMES GENETICS 2019; 9:3867-3875. [PMID: 31551287 PMCID: PMC6829149 DOI: 10.1534/g3.119.400656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Poecilia reticulata is one of the most popular ornamental fish species with a higher demand for males due to their large colorful fins. The objectives of this study were mapping of the sex-determining (SD) region on linkage group 12 of guppy, and identification of a sex specific marker. We generated eight polymorphic microsatellite markers distributed along the distal 5.4 Mbp sequence of the previously identified SD region on linkage group (LG) 12. The markers were tested for association with sex in 156 individuals of the Red Blonde and Flame strains, and 126 progeny of four full-sibs Red Blonde families. A male-specific allele was found for microsatellite gu1066 at position of 25.3 Mbp on LG12 for both strains, and gu832 at position 24.4 Mbp for the Flame strain. Thus, a region of 0.9 Mbp between these markers, harboring 27 annotated genes, was selected for analysis. Based on association of copy number variation and sex determination we mapped a duplicated region between LGs 9 and 12, of 1.26 Mbp, containing 59 genes on LG12. The common interval between the segment bounded by gu1066 and gu832, and the duplicated region of 0.43 Mbp on LG12 harbors 11 genes of which 6 have multiple copies (54%). Growth arrest and DNA damage inducible gamma-like (GADD45G-like) is a plausible positional and functional candidate gene for its role in male fertility. We characterized the genomic structure of the gene in guppy, and found two isoforms; but no sex-biased differences were evident in genomic sequence and gene expression.
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5
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Komissarov A, Vij S, Yurchenko A, Trifonov V, Thevasagayam N, Saju J, Sridatta PSR, Purushothaman K, Graphodatsky A, Orbán L, Kuznetsova I. B Chromosomes of the Asian Seabass ( Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations. Genes (Basel) 2018; 9:E464. [PMID: 30241368 PMCID: PMC6211105 DOI: 10.3390/genes9100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 12/01/2022] Open
Abstract
The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.
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Affiliation(s)
- Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
| | - Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- School of Applied Science, Republic Polytechnic 9 Woodlands Avenue 9, Singapore 738964, Singapore.
| | - Andrey Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Natascha Thevasagayam
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | - Jolly Saju
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | | | - Kathiresan Purushothaman
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
| | - Alexander Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Department of Animal Sciences, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Hungary.
- Center for Comparative Genomics, Murdoch University, 6150 Murdoch, Australia.
| | - Inna Kuznetsova
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
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6
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Tan TK, Tan KY, Hari R, Mohamed Yusoff A, Wong GJ, Siow CC, Mutha NVR, Rayko M, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Paterson IC, Warren WC, Johnson WE, O'Brien SJ, Choo SW. PGD: a pangolin genome hub for the research community. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw063. [PMID: 27616775 PMCID: PMC5018392 DOI: 10.1093/database/baw063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 04/11/2016] [Indexed: 01/01/2023]
Abstract
Pangolins (order Pholidota) are the only mammals covered by scales. We have recently sequenced and analyzed the genomes of two critically endangered Asian pangolin species, namely the Malayan pangolin (Manis javanica) and the Chinese pangolin (Manis pentadactyla). These complete genome sequences will serve as reference sequences for future research to address issues of species conservation and to advance knowledge in mammalian biology and evolution. To further facilitate the global research effort in pangolin biology, we developed the Pangolin Genome Database (PGD), as a future hub for hosting pangolin genomic and transcriptomic data and annotations, and with useful analysis tools for the research community. Currently, the PGD provides the reference pangolin genome and transcriptome data, gene sequences and functional information, expressed transcripts, pseudogenes, genomic variations, organ-specific expression data and other useful annotations. We anticipate that the PGD will be an invaluable platform for researchers who are interested in pangolin and mammalian research. We will continue updating this hub by including more data, annotation and analysis tools particularly from our research consortium.Database URL: http://pangolin-genome.um.edu.my.
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Affiliation(s)
- Tze King Tan
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ka Yun Tan
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia Institute of Biology Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur Malaysia
| | - Ranjeev Hari
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Aini Mohamed Yusoff
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Guat Jah Wong
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Cheuk Chuen Siow
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Naresh V R Mutha
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mike Rayko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia
| | - Ian C Paterson
- Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia Oral Cancer Research and Coordinating Centre, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St Louis, MO 63108, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, Front Royal, Virginia 22630, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA
| | - Siew Woh Choo
- Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, 50603 Kuala Lumpur, Malaysia
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7
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Dor L, Shirak A, Rosenfeld H, Ashkenazi IM, Band MR, Korol A, Ronin Y, Seroussi E, Weller JI, Ron M. Identification of the sex-determining region in flathead grey mullet (Mugil cephalus). Anim Genet 2016; 47:698-707. [PMID: 27611243 DOI: 10.1111/age.12486] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2016] [Indexed: 11/29/2022]
Abstract
Elucidation of the sex-determination mechanism in flathead grey mullet (Mugil cephalus) is required to exploit its economic potential by production of genetically determined monosex populations and application of hormonal treatment to parents rather than to the marketed progeny. Our objective was to construct a first-generation linkage map of the M. cephalus in order to identify the sex-determining region and sex-determination system. Deep-sequencing data of a single male was assembled and aligned to the genome of Nile tilapia (Oreochromis niloticus). A total 245 M. cephalus microsatellite markers were designed, spanning the syntenic tilapia genome assembly at intervals of 10 Mb. In the mapping family of full-sib progeny, 156 segregating markers were used to construct a first-generation linkage map of 24 linkage groups (LGs), corresponding to the number of chromosomes. The linkage map spanned approximately 1200 cM with an average inter-marker distance of 10.6 cM. Markers segregating on LG9 in two independent mapping families showed nearly complete concordance with gender (R2 = 0.95). The sex determining locus was fine mapped within an interval of 8.6 cM on LG9. The sex of offspring was determined only by the alleles transmitted from the father, thus indicating an XY sex-determination system.
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Affiliation(s)
- L Dor
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, 50250, Israel.,Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - A Shirak
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - H Rosenfeld
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, 88112, Israel
| | - I M Ashkenazi
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, 88112, Israel
| | - M R Band
- The Carver Biotechnology Center, University of Illinois, Urbana, IL, 61801, USA
| | - A Korol
- Faculty of Science, Institute of Evolution, University Haifa, Haifa, 31905, Israel
| | - Y Ronin
- Faculty of Science, Institute of Evolution, University Haifa, Haifa, 31905, Israel
| | - E Seroussi
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - J I Weller
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, 50250, Israel
| | - M Ron
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, 50250, Israel.
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8
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AlMomin S, Kumar V, Al-Amad S, Al-Hussaini M, Dashti T, Al-Enezi K, Akbar A. Draft genome sequence of the silver pomfret fish, Pampus argenteus. Genome 2015; 59:51-8. [PMID: 26692342 DOI: 10.1139/gen-2015-0056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.
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Affiliation(s)
- Sabah AlMomin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Vinod Kumar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Sami Al-Amad
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Mohsen Al-Hussaini
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Talal Dashti
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Khaznah Al-Enezi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Abrar Akbar
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait.,Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
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9
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Böhne A, Sengstag T, Salzburger W. Comparative transcriptomics in East African cichlids reveals sex- and species-specific expression and new candidates for sex differentiation in fishes. Genome Biol Evol 2015; 6:2567-85. [PMID: 25364805 PMCID: PMC4202336 DOI: 10.1093/gbe/evu200] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Males and females of the same species differ largely in gene expression, which accounts for most of the morphological and physiological differences and sex-specific phenotypes. Here, we analyzed sex-specific gene expression in the brain and the gonads of cichlid fishes from Lake Tanganyika belonging to four different lineages, so-called tribes (Eretmodini, Ectodini, Haplochromini, and Lamprologini), using the outgroup Nile tilapia (Oreochromis niloticus) as reference. The comparison between male and female brains revealed few differences between the sexes, consistent in all investigated species. The gonads, on the other hand, showed a large fraction of differentially expressed transcripts with the majority of them showing the same direction of expression in all four species. All here-studied cichlids, especially the three investigated mouth-breeding species, showed a trend toward more male- than female biased transcripts. Transcripts, which were female-biased in expression in all four species, were overrepresented on linkage group (LG)1 in the reference genome and common male-biased transcripts showed accumulation on LG23, the presumable sex chromosomes of the Nile tilapia. Sex-specific transcripts contained candidate genes for sex determination and differentiation in fishes,especially members of the transforming growth factor-b-superfamily and the Wnt-pathway and also prominent members of the sox-, dm-domain-, and high mobility group-box families. We further confirmed our previous finding on species/lineage-specific gene expression shifts in the sex steroid pathway, including synthesizing enzymes as the aromatase cyp19a1 and estrogen and androgen receptors.
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Affiliation(s)
- Astrid Böhne
- Zoological Institute, University of Basel, Switzerland
- *Corresponding author: E-mail:
| | - Thierry Sengstag
- SIB Swiss Institute of Bioinformatics and sciCORE Computing Center, University of Basel, Switzerland
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Kuznetsova IS, Thevasagayam NM, Sridatta PSR, Komissarov AS, Saju JM, Ngoh SY, Jiang J, Shen X, Orbán L. Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome. Front Genet 2014; 5:223. [PMID: 25120555 PMCID: PMC4110674 DOI: 10.3389/fgene.2014.00223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/27/2014] [Indexed: 02/05/2023] Open
Abstract
As part of our Asian seabass genome project, we are generating an inventory of repeat elements in the genome and transcriptome. The karyotype showed a diploid number of 2n = 24 chromosomes with a variable number of B-chromosomes. The transcriptome and genome of Asian seabass were searched for repetitive elements with experimental and bioinformatics tools. Six different types of repeats constituting 8–14% of the genome were characterized. Repetitive elements were clustered in the pericentromeric heterochromatin of all chromosomes, but some of them were preferentially accumulated in pretelomeric and pericentromeric regions of several chromosomes pairs and have chromosomes specific arrangement. From the dispersed class of fish-specific non-LTR retrotransposon elements Rex1 and MAUI-like repeats were analyzed. They were wide-spread both in the genome and transcriptome, accumulated on the pericentromeric and peritelomeric areas of all chromosomes. Every analyzed repeat was represented in the Asian seabass transcriptome, some showed differential expression between the gonads. The other group of repeats analyzed belongs to the rRNA multigene family. FISH signal for 5S rDNA was located on a single pair of chromosomes, whereas that for 18S rDNA was found on two pairs. A BAC-derived contig containing rDNA was sequenced and assembled into a scaffold containing incomplete fragments of 18S rDNA. Their assembly and chromosomal position revealed that this part of Asian seabass genome is extremely rich in repeats containing evolutionarily conserved and novel sequences. In summary, transcriptome assemblies and cDNA data are suitable for the identification of repetitive DNA from unknown genomes and for comparative investigation of conserved elements between teleosts and other vertebrates.
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Affiliation(s)
- Inna S Kuznetsova
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; Institute of Cytology of the Russian Academy of Sciences St-Petersburg, Russia
| | - Natascha M Thevasagayam
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - Prakki S R Sridatta
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - Aleksey S Komissarov
- Institute of Cytology of the Russian Academy of Sciences St-Petersburg, Russia ; Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University St Petersburg, Russia
| | - Jolly M Saju
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - Si Y Ngoh
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; School of Biological Sciences, Nanyang Technological University Singapore, Republic of Singapore
| | - Junhui Jiang
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; Agri-Food and Veterinary Authority of Singapore Singapore, Republic of Singapore
| | - Xueyan Shen
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - László Orbán
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia Keszthely, Hungary ; Department of Biological Sciences, National University of Singapore Singapore, Republic of Singapore
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11
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Dor L, Shirak A, Gorshkov S, Band MR, Korol A, Ronin Y, Curzon A, Hulata G, Seroussi E, Ron M. Construction of a microsatellites-based linkage map for the white grouper (Epinephelus aeneus). G3 (BETHESDA, MD.) 2014; 4:1455-64. [PMID: 24902605 PMCID: PMC4132176 DOI: 10.1534/g3.114.011387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/01/2014] [Indexed: 02/06/2023]
Abstract
The white grouper (Epinephelus aeneus) is a promising candidate for domestication and aquaculture due to its fast growth, excellent taste, and high market price. A linkage map is an essential framework for mapping quantitative trait loci for economic traits and the study of genome evolution. DNA of a single individual was deep-sequenced, and microsatellite markers were identified in 177 of the largest scaffolds of the sequence assembly. The success rate of developing polymorphic homologous markers was 94.9% compared with 63.1% of heterologous markers from other grouper species. Of the 12 adult mature fish present in the broodstock tank, two males and two females were identified as parents of the assigned offspring by parenthood analysis using 34 heterologous markers. A single full-sib family of 48 individuals was established for the construction of first-generation linkage maps based on genotyping data of 222 microsatellites. The markers were assigned to 24 linkage groups in accordance to the 24 chromosomal pairs. The female and male maps consisting of 203 and 202 markers spanned 1053 and 886 cM, with an average intermarker distance of 5.8 and 5.0 cM, respectively. Mapping of markers to linkage groups ends was enriched by using markers originating from scaffolds harboring telomeric repeat-containing RNA. Comparative mapping showed high synteny relationships among the white grouper, kelp grouper (E. bruneus), orange-spotted grouper (E. coioides), and Nile tilapia (Oreochromis niloticus). Thus, it would be useful to integrate the markers that were developed for different groupers, depending on sharing of sequence data, into a comprehensive consensus map.
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Affiliation(s)
- Lior Dor
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Sergei Gorshkov
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Mark R Band
- The Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Abraham Korol
- University Haifa, Institute of Evolution, of Haifa 3498838, Israel
| | - Yefim Ronin
- University Haifa, Institute of Evolution, of Haifa 3498838, Israel
| | - Arie Curzon
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Gideon Hulata
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
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12
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Valente GT, Conte MA, Fantinatti BE, Cabral-de-Mello DC, Carvalho RF, Vicari MR, Kocher TD, Martins C. Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses. Mol Biol Evol 2014; 31:2061-72. [DOI: 10.1093/molbev/msu148] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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13
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Fuji K, Koyama T, Kai W, Kubota S, Yoshida K, Ozaki A, Aoki JY, Kawabata Y, Araki K, Tsuzaki T, Okamoto N, Sakamoto T. Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata. BMC Res Notes 2014; 7:200. [PMID: 24684753 PMCID: PMC4230249 DOI: 10.1186/1756-0500-7-200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 02/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Japanese amberjack/yellowtail (Seriola quinqueradiata) is a commonly cultured marine fish in Japan. For cost effective fish production, a breeding program that increases commercially important traits is one of the major solutions. In selective breeding, information of genetic markers is useful and sufficient to identify individuals carrying advantageous traits but if the aim is to determine the genetic basis of the trait, large insert genomic DNA libraries are essential. In this study, toward prospective understanding of genetic basis of several economically important traits, we constructed a high-coverage bacterial artificial chromosome (BAC) library, obtained sequences from the BAC-end, and constructed comprehensive female and male linkage maps of yellowtail using Simple Sequence Repeat (SSR) markers developed from the BAC-end sequences and a yellowtail genomic library. RESULTS The total insert length of the BAC library we constructed here was estimated to be approximately 11 Gb and hence 16-times larger than the yellowtail genome. Sequencing of the BAC-ends showed a low fraction of repetitive sequences comparable to that in Tetraodon and fugu. A total of 837 SSR markers developed here were distributed among 24 linkage groups spanning 1,026.70 and 1,057.83 cM with an average interval of 4.96 and 4.32 cM in female and male map respectively without any segregation distortion. Oxford grids suggested conserved synteny between yellowtail and stickleback. CONCLUSIONS In addition to characteristics of yellowtail genome such as low repetitive sequences and conserved synteny with stickleback, our genomic and genetic resources constructed and revealed here will be powerful tools for the yellowtail breeding program and also for studies regarding the genetic basis of traits.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo 108-8477, Japan.
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14
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Chen GL, Chang YJ, Hsueh CH. PRAP: an ab initio software package for automated genome-wide analysis of DNA repeats for prokaryotes. Bioinformatics 2013; 29:2683-9. [DOI: 10.1093/bioinformatics/btt482] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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15
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Yoshida K, Terai Y, Mizoiri S, Aibara M, Nishihara H, Watanabe M, Kuroiwa A, Hirai H, Hirai Y, Matsuda Y, Okada N. B chromosomes have a functional effect on female sex determination in Lake Victoria cichlid fishes. PLoS Genet 2011; 7:e1002203. [PMID: 21876673 PMCID: PMC3158035 DOI: 10.1371/journal.pgen.1002203] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/08/2011] [Indexed: 11/19/2022] Open
Abstract
The endemic cichlid fishes in Lake Victoria are a model system for speciation through adaptive radiation. Although the evolution of the sex-determination system may also play a role in speciation, little is known about the sex-determination system of Lake Victoria cichlids. To understand the evolution of the sex-determination system in these fish, we performed cytogenetic analysis in 11 cichlid species from Lake Victoria. B chromosomes, which are present in addition to standard chromosomes, were found at a high prevalence rate (85%) in these cichlids. In one species, B chromosomes were female-specific. Cross-breeding using females with and without the B chromosomes demonstrated that the presence of the B chromosomes leads to a female-biased sex ratio in this species. Although B chromosomes were believed to be selfish genetic elements with little effect on phenotype and to lack protein-coding genes, the present study provides evidence that B chromosomes have a functional effect on female sex determination. FISH analysis using a BAC clone containing B chromosome DNA suggested that the B chromosomes are derived from sex chromosomes. Determination of the nucleotide sequences of this clone (104.5 kb) revealed the presence of several protein-coding genes in the B chromosome, suggesting that B chromosomes have the potential to contain functional genes. Because some sex chromosomes in amphibians and arthropods are thought to be derived from B chromosomes, the B chromosomes in Lake Victoria cichlids may represent an evolutionary transition toward the generation of sex chromosomes.
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Affiliation(s)
- Kohta Yoshida
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yohey Terai
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Shinji Mizoiri
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Mitsuto Aibara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Masakatsu Watanabe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Asato Kuroiwa
- Laboratory of Animal Cytogenetics, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Yoichi Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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16
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Kuhl H, Tine M, Beck A, Timmermann B, Kodira C, Reinhardt R. Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones. Genomics 2011; 98:202-12. [PMID: 21693181 DOI: 10.1016/j.ygeno.2011.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 05/31/2011] [Accepted: 06/03/2011] [Indexed: 02/02/2023]
Abstract
Dicentrarchus labrax is one of the major marine aquaculture species in the European Union. In this study, we have developed a directed-sequencing strategy to sequence three sea bass chromosomes and compared results with other teleosts. Three BAC DNA pools were created from sea bass BAC clones that mapped to stickleback chromosomes/groups V, XVII and XXI. The pools were sequenced to 17-39x coverage by pyrosequencing. Data assembly was supported by Sanger reads and mate pair data and resulted in superscaffolds of 13.2 Mb, 17.5 Mb and 13.7 Mb respectively. Annotation features of the superscaffolds include 1477 genes. We analyzed size change of exon, intron and intergenic sequence between teleost species and deduced a simple model for the evolution of genome composition in teleost lineage. Combination of second generation sequencing technologies, Sanger sequencing and genome partitioning strategies allows "high-quality draft assemblies" of chromosome-sized superscaffolds, which are crucial for the prediction and annotation of complete genes.
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Affiliation(s)
- Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany.
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17
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Xu P, Li J, Li Y, Cui R, Wang J, Wang J, Zhang Y, Zhao Z, Sun X. Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences. BMC Genomics 2011; 12:188. [PMID: 21492448 PMCID: PMC3083359 DOI: 10.1186/1471-2164-12-188] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 04/14/2011] [Indexed: 12/26/2022] Open
Abstract
Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of the zebrafish genome. BES of common carp are tremendous tools for comparative mapping between the two closely related species, zebrafish and common carp, which should facilitate both structural and functional genome analysis in common carp.
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Affiliation(s)
- Peng Xu
- The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China.
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18
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Soler L, Conte MA, Katagiri T, Howe AE, Lee BY, Amemiya C, Stuart A, Dossat C, Poulain J, Johnson J, Di Palma F, Lindblad-Toh K, Baroiller JF, D'Cotta H, Ozouf-Costaz C, Kocher TD. Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus). BMC Genomics 2010; 11:636. [PMID: 21080946 PMCID: PMC3018143 DOI: 10.1186/1471-2164-11-636] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 11/16/2010] [Indexed: 01/07/2023] Open
Abstract
Background The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species. Results We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies. Conclusions Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.
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Affiliation(s)
- Lucile Soler
- CIRAD-PERSYST, Aquaculture Research Unit, TA B-20/A, Campus International de Baillarguet, 34398 Montpellier cedex 5, France
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