DOI: 10.1016/s0014-5793(00)01659-8. Fugu: a compact vertebrate reference genome

Fugu: a compact vertebrate reference genome

10.1016/s0014-5793(00)01659-8

Crossref journal-article

Wiley

FEBS Letters (311)

Abstract

At 400 Mb, the Japanese pufferfish, Fugu rubripes, has the smallest vertebrate genome but has a similar gene repertoire to other vertebrates. Its genes are densely packed with short intergenic and intronic sequences devoid of repetitive elements. It likely has a mutational bias towards DNA elimination and is probably close to a ‘minimal’ vertebrate genome. As such it is a useful reference genome for gene discovery and gene validation in other vertebrates. Its usefulness in the discovery of conserved regulatory elements has already been demonstrated. The Fugu genome sequence is a good complement to genetic studies in other vertebrates.

Bibliography

Venkatesh, B., Gilligan, P., & Brenner, S. (2000). Fugu: a compact vertebrate reference genome. FEBS Letters, 476(1â2), 3â7. Portico.

Authors 3

Byrappa Venkatesh (first)
Patrick Gilligan (additional)
Sydney Brenner (additional)

References 48 Referenced 111

10.1038/366265a0
Nelson J.S. (1994) Fishes of the World John Wiley New York.
10.1073/pnas.96.18.10267
Leis J.M. (1983) in: Ontogeny and Systematics of Fishes (Moser H.G. Ed.) Special Publication No. 1 pp. 459–463. Am. Soc. Ichthyol. Herpetol.
10.1101/gr.9.10.960
10.1016/S0378-1119(98)00296-0
10.1016/S0378-1119(98)00600-3
10.1126/science.282.5394.1711
10.1016/0888-7543(95)80044-M
10.1101/gr.6.12.1207
10.1006/jmbi.1996.0347
10.1006/geno.1996.0406
10.1016/S0378-1119(97)00064-4
10.1073/pnas.95.9.5178
10.1126/science.287.5455.1060
10.1038/ng0595-67
10.1073/pnas.93.16.8485
10.1006/geno.1997.4913
10.1016/S0378-1119(97)00423-X
10.1016/S0378-1119(98)00495-8
10.1016/S0378-1119(98)00010-9
10.1016/S0378-1119(98)00032-8
10.1006/geno.1998.5732
10.1101/gr.9.3.242
10.1073/pnas.93.4.1366
10.1073/pnas.94.23.12462
10.1073/pnas.95.22.13068
10.1101/gr.9.3.251
10.1038/990031
10.1126/science.282.5396.2012
10.1126/science.287.5461.2185
10.1101/gr.6.12.1185
10.1038/ng0597-79
10.1101/gr.9.5.437
10.1093/hmg/8.7.1313
10.1038/35001596
10.1073/pnas.92.5.1684
10.1242/dev.124.20.3929
10.1242/dev.125.14.2735
10.1016/0300-9629(76)90063-3 / Comp. Biochem. Physiol. by Hinegardner R. (1976)
{'key': 'e_1_2_8_42_1', 'first-page': '447', 'volume': '92', 'author': 'Olmo E.', 'year': '1989', 'journal-title': 'Comp. Biochem. Physiol.'} / Comp. Biochem. Physiol. by Olmo E. (1989)
10.1002/cyto.990100606
10.1086/282801
Bloom S.E. Delany M.E. and Muscarella D.E. (1993) in: Manipulation of the Avian Genome (Etches R.J. and Gibbons A.M.V. Eds.) pp. 39–59. CRC Press Boca Raton FL.
10.1016/S0168-9525(98)01506-6
10.1101/gr.8.1.9
{'key': 'e_1_2_8_48_1', 'first-page': '346', 'volume': '1', 'author': 'Ozato K.', 'year': '1992', 'journal-title': 'Mol. Mar. Biol. Biotech.'} / Mol. Mar. Biol. Biotech. by Ozato K. (1992)
10.2331/fishsci.61.594

Dates

Type	When
Created	23 years, 1 month ago (July 25, 2002, 4:35 p.m.)
Deposited	1 year, 11 months ago (Sept. 16, 2023, 1:47 p.m.)
Indexed	2 weeks, 6 days ago (Aug. 7, 2025, 4:33 p.m.)
Issued	25 years, 2 months ago (June 26, 2000)
Published	25 years, 2 months ago (June 26, 2000)
Published Online	25 years, 2 months ago (June 26, 2000)
Published Print	25 years, 1 month ago (June 30, 2000)

Funders 0

None

BibTeX

@article{Venkatesh_2000, title={Fugu: a compact vertebrate reference genome}, volume={476}, ISSN={1873-3468}, url={http://dx.doi.org/10.1016/s0014-5793(00)01659-8}, DOI={10.1016/s0014-5793(00)01659-8}, number={1–2}, journal={FEBS Letters}, publisher={Wiley}, author={Venkatesh, Byrappa and Gilligan, Patrick and Brenner, Sydney}, year={2000}, month=jun, pages={3–7} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        7
      ]
    ],
    "date-time": "2025-08-07T20:33:46Z",
    "timestamp": 1754598826376
  },
  "reference-count": 48,
  "publisher": "Wiley",
  "issue": "1-2",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2000,
            6,
            26
          ]
        ],
        "date-time": "2000-06-26T00:00:00Z",
        "timestamp": 961977600000
      },
      "content-version": "vor",
      "delay-in-days": 0,
      "URL": "http://onlinelibrary.wiley.com/termsAndConditions#vor"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2000,
        6,
        30
      ]
    ]
  },
  "abstract": "<jats:p>At 400 Mb, the Japanese pufferfish, <jats:italic>Fugu rubripes</jats:italic>, has the smallest vertebrate genome but has a similar gene repertoire to other vertebrates. Its genes are densely packed with short intergenic and intronic sequences devoid of repetitive elements. It likely has a mutational bias towards DNA elimination and is probably close to a \u2018minimal\u2019 vertebrate genome. As such it is a useful reference genome for gene discovery and gene validation in other vertebrates. Its usefulness in the discovery of conserved regulatory elements has already been demonstrated. The Fugu genome sequence is a good complement to genetic studies in other vertebrates.</jats:p>",
  "DOI": "10.1016/s0014-5793(00)01659-8",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2002,
        7,
        25
      ]
    ],
    "date-time": "2002-07-25T20:35:07Z",
    "timestamp": 1027629307000
  },
  "page": "3-7",
  "source": "Crossref",
  "is-referenced-by-count": 111,
  "title": "Fugu: a compact vertebrate reference genome",
  "prefix": "10.1002",
  "volume": "476",
  "author": [
    {
      "given": "Byrappa",
      "family": "Venkatesh",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Patrick",
      "family": "Gilligan",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Sydney",
      "family": "Brenner",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "311",
  "published-online": {
    "date-parts": [
      [
        2000,
        6,
        26
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_2_8_2_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/366265a0"
    },
    {
      "key": "e_1_2_8_3_1",
      "unstructured": "Nelson J.S. (1994) Fishes of the World John Wiley New York."
    },
    {
      "key": "e_1_2_8_4_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.96.18.10267"
    },
    {
      "key": "e_1_2_8_5_1",
      "unstructured": "Leis J.M. (1983) in: Ontogeny and Systematics of Fishes (Moser H.G. Ed.) Special Publication No. 1 pp. 459&#x2013;463. Am. Soc. Ichthyol. Herpetol."
    },
    {
      "key": "e_1_2_8_6_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.9.10.960"
    },
    {
      "key": "e_1_2_8_7_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0378-1119(98)00296-0"
    },
    {
      "key": "e_1_2_8_8_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0378-1119(98)00600-3"
    },
    {
      "key": "e_1_2_8_9_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.282.5394.1711"
    },
    {
      "key": "e_1_2_8_10_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/0888-7543(95)80044-M"
    },
    {
      "key": "e_1_2_8_11_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.6.12.1207"
    },
    {
      "key": "e_1_2_8_12_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/jmbi.1996.0347"
    },
    {
      "key": "e_1_2_8_13_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/geno.1996.0406"
    },
    {
      "key": "e_1_2_8_14_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0378-1119(97)00064-4"
    },
    {
      "key": "e_1_2_8_15_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.95.9.5178"
    },
    {
      "key": "e_1_2_8_16_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.287.5455.1060"
    },
    {
      "key": "e_1_2_8_17_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng0595-67"
    },
    {
      "key": "e_1_2_8_18_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.93.16.8485"
    },
    {
      "key": "e_1_2_8_19_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/geno.1997.4913"
    },
    {
      "key": "e_1_2_8_20_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0378-1119(97)00423-X"
    },
    {
      "key": "e_1_2_8_21_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0378-1119(98)00495-8"
    },
    {
      "key": "e_1_2_8_22_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0378-1119(98)00010-9"
    },
    {
      "key": "e_1_2_8_23_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0378-1119(98)00032-8"
    },
    {
      "key": "e_1_2_8_24_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1006/geno.1998.5732"
    },
    {
      "key": "e_1_2_8_25_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.9.3.242"
    },
    {
      "key": "e_1_2_8_26_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.93.4.1366"
    },
    {
      "key": "e_1_2_8_27_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.94.23.12462"
    },
    {
      "key": "e_1_2_8_28_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.95.22.13068"
    },
    {
      "key": "e_1_2_8_29_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.9.3.251"
    },
    {
      "key": "e_1_2_8_30_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/990031"
    },
    {
      "key": "e_1_2_8_31_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.282.5396.2012"
    },
    {
      "key": "e_1_2_8_32_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.287.5461.2185"
    },
    {
      "key": "e_1_2_8_33_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.6.12.1185"
    },
    {
      "key": "e_1_2_8_34_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng0597-79"
    },
    {
      "key": "e_1_2_8_35_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.9.5.437"
    },
    {
      "key": "e_1_2_8_36_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1093/hmg/8.7.1313"
    },
    {
      "key": "e_1_2_8_37_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/35001596"
    },
    {
      "key": "e_1_2_8_38_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.92.5.1684"
    },
    {
      "key": "e_1_2_8_39_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1242/dev.124.20.3929"
    },
    {
      "key": "e_1_2_8_40_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1242/dev.125.14.2735"
    },
    {
      "key": "e_1_2_8_41_1",
      "doi-asserted-by": "crossref",
      "first-page": "367",
      "DOI": "10.1016/0300-9629(76)90063-3",
      "volume": "55",
      "author": "Hinegardner R.",
      "year": "1976",
      "journal-title": "Comp. Biochem. Physiol."
    },
    {
      "key": "e_1_2_8_42_1",
      "first-page": "447",
      "volume": "92",
      "author": "Olmo E.",
      "year": "1989",
      "journal-title": "Comp. Biochem. Physiol."
    },
    {
      "key": "e_1_2_8_43_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1002/cyto.990100606"
    },
    {
      "key": "e_1_2_8_44_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1086/282801"
    },
    {
      "key": "e_1_2_8_45_1",
      "unstructured": "Bloom S.E. Delany M.E. and Muscarella D.E. (1993) in: Manipulation of the Avian Genome (Etches R.J. and Gibbons A.M.V. Eds.) pp. 39&#x2013;59. CRC Press Boca Raton FL."
    },
    {
      "key": "e_1_2_8_46_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0168-9525(98)01506-6"
    },
    {
      "key": "e_1_2_8_47_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.1101/gr.8.1.9"
    },
    {
      "key": "e_1_2_8_48_1",
      "first-page": "346",
      "volume": "1",
      "author": "Ozato K.",
      "year": "1992",
      "journal-title": "Mol. Mar. Biol. Biotech."
    },
    {
      "key": "e_1_2_8_49_1",
      "doi-asserted-by": "publisher",
      "DOI": "10.2331/fishsci.61.594"
    }
  ],
  "container-title": "FEBS Letters",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1016%2FS0014-5793%2800%2901659-8",
      "content-type": "application/pdf",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1016%2FS0014-5793(00)01659-8",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/S0014-5793%2800%2901659-8",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2023,
        9,
        16
      ]
    ],
    "date-time": "2023-09-16T17:47:09Z",
    "timestamp": 1694886429000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://febs.onlinelibrary.wiley.com/doi/10.1016/S0014-5793%2800%2901659-8"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2000,
        6,
        26
      ]
    ]
  },
  "references-count": 48,
  "journal-issue": {
    "issue": "1-2",
    "published-print": {
      "date-parts": [
        [
          2000,
          6,
          30
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1016/S0014-5793(00)01659-8"
  ],
  "URL": "http://dx.doi.org/10.1016/S0014-5793(00)01659-8",
  "relation": {},
  "ISSN": [
    "0014-5793",
    "1873-3468"
  ],
  "subject": [],
  "container-title-short": "FEBS Letters",
  "published": {
    "date-parts": [
      [
        2000,
        6,
        26
      ]
    ]
  }
}