葡萄基因组测定完成 2007年8月28日一项由法国科学家领导的最新研究捍卫了法国作为“葡萄酒之都"的荣誉, 他们完整测定了一种葡萄的基因组。葡萄也由此成为人类完成基因测序的第一种水果作物 和第四种开花植物(其它3种分别是小麦、拟南芥和白杨木),这有望加深科学家对开花植 物进化过程的理解。相关论文8月26日在线发表于《自然》杂志。 该项研究由法国和意大利组成的科学家团队完成,而领导他们的是法国 Genoscope国家 基因测序中心的遗传学家 Patrick Wicker。他们完整分析了制造勃艮第和香槟酒的主要原 料——“黑比诺”( Pinot noir)葡萄的基因序列 利用“黑比诺”变异较少的特点,研究人员培育出了一种稳定的葡萄种系PN40024。随后, 他们将PN40024葡萄的DNA分割成几百万个片断并分别进行了测序,再利用计算机程序 将基因编码结合起来,从而得到了完整的基因组。不出所料,硏究人员发现,该葡萄基因组 的300多个基因中有许多都是用来制造赋予葡萄香味的萜类化合物和丹宁酸(共有大约5 亿个碱基对),而且这一比例大大超过了其他的植物 研究人员此次专门研究了70至80个制造萜类化合物的基因,目的是为了能够通过基因改 造,开发味道更加独特的葡萄酒,并增强葡萄对害虫和有害物(比如霉菌)的抵抗能力。 此次葡萄基因组的测定有助于科学家了解开花植物的一个关键进化过程,也就是大约25 亿年雨双子吐植物和单子叶植物的分化。此次测定的葡萄基因组与之前的小麦基因组对 表明,双子叶植物的基因组有大规模复制成为原来3倍的明显特点和标记 不过,一位 Genoscope研究人员 Jean Weissenbach指出,遗传学家此次研究成果和认 识并不能替代进化学家和葡萄酒制造者长期以来的传统观点。他说,“我们能够创造出具有 不同香味的葡萄变种,但最终葡萄酒的品质则完全是另一回事。”(科学网任霄鹏/编译) Genome projects were initiated on grapevine(Vitis vinifera L, 2n=38, genome size 475 Annotated genes Annotated transcripts 26,346 Average number of coding exons per gene 5.95 Median gene size(bp) Average CDS size(bp) 1.137 Median exon size(bp) This Grapevine genome sequence analysis results from a collaboration between Genoscope NRA, the Institute of Applied Genomics and a consortium of italian groups. The sequence data(12X coverage)was generated by Genoscope, The Institute of Applied Genomics and the University of Verona. The assembly was done by The Institute of Applied Genomics. The gene predictions were perfomed using the GAZE computational framework This project was financed by the French Ministry of Higher Education and Research, the Consortium National de Recherche en Genomique, the Agence Nationale de la recherche NRA, the italian Ministry of Agriculture(VIGNA-CRA), and Regione Autonoma Friuli Venezia
葡萄基因组测定完成 2007年8月28日 项由法国科学家领导的最新研究捍卫了法国作 “葡萄酒之都”的荣誉， 他们完整测定了一 葡萄的基因组 葡萄也由此成为人类完成基因测序的第一种水果作物 和第四种开花植物（其它 3 种分别是小麦、拟南芥和白杨木）， 有望加深科学家对开花植 物进化过程的理解。相关论文 8 月 26 日在线发表于《自然》杂志。 该项研究由法国和意 利组成的科学家团队完成，而领导他们的是法国 Genoscope 国家 基因测序中心的遗传学家 Patrick Wincker。他们完整分析了制造勃艮第和香槟酒的主要原 料——“黑比诺”（Pinot Noir）葡萄的基因序列。 利用“黑比诺”变异较少的特点，研究人员培育出了一种稳定的葡萄种系 PN 40024。随后， 他们将 PN 40024 葡萄的 DNA 分割成几百万 片断并分别进行了测序，再利用计算机程序 将基因编码结合起来，从而得到了完整的基因组。不出所料，研究人员发现，该葡萄基因组 的 3000 个基因中有许多都是用来制造赋予葡萄香味的萜类化合物和丹宁酸（共有大约 5 亿个碱基对），而且这一比例大大超过了其他的植物。 研究人员此次专门研究了 70 至 80 个制造萜类化合物的基因，目的是为了能够通过基因改 造，开发味道 加独特的葡萄酒，并增强葡萄对害虫和有害物（比如霉菌）的抵抗能力。 此次葡萄基因组的测定有助于科学家了解开花植物的一个关键进化过程，也就是大约 2.5 亿年 双子叶植物和单子叶植物的分化。此次测定的葡萄基因组与之前的小麦基因组对比 表明，双子叶植物的基因组有大规模复制成为原来 3 倍的明显特点和标记。 不过，一位 Genoscope 研究人员 Jean Weissenbach 指出，遗传学家此次研究成果和认 识并不能替代进化学家和葡萄酒制造者长期以来的传统观点。他说，“我们能够创造出具有 不同香味的葡萄变种，但最终葡萄酒的品质则完全是另一回事。”（科学网 任霄鹏/编译） Genome projects were initiated on grapevine (Vitis vinifera L., 2n=38, genome size 475 Mb) Annotated genes 26,346 Annotated transcripts 26,346 Average number of coding exons per gene 5.95 Median gene size (bp) 3,572 Average CDS size (bp) 1,137 Median exon size (bp) 122 This Grapevine genome sequence analysis results from a collaboration between Genoscope, INRA, the Institute of Applied Genomics and a consortium of Italian groups. The sequence data (12X coverage) was generated by Genoscope, The Institute of Applied Genomics and the University of Verona. The assembly was done by The Institute of Applied Genomics. The gene predictions were performed using the GAZE computational framework. This project was financed by the French Ministry of Higher Education and Research, the Consortium National de Recherche en Génomique, the Agence Nationale de la Recherche, INRA, the Italian Ministry of Agriculture (VIGNA-CRA), and Regione Autonoma Friuli Venezia
Giulia together with a consortium of private companies and banks(IGA) Nature 449, 463-467(27 September 2007)I doi: 10.1038/nature 06148: Received 5 April 2007: Accepted 7 August 2007: Published online 26 August 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Olivier Jaillon.a, Jean-Marc Auryll, Benjam in Noel, Alberto Policriti2-, Christian Clepet- Alberto Casagrande., Nathalie Choisnel4, Sebastien Aubourg#, Nicola Vitulo 515, Claire Jubin Alessandro Vezzi5l5, Fabrice Legeai, Philippe Hugueney, Corinne Dasilva, David Horner2, 5, Erica Mica2 1, Delphine Jublot=, Julie Poulain Clemence Bruyere#, Alain Billault1 Beatrice Segurens-, Michel Gouyvenoux Edgardo Ugarte - Federica Cattonaros, veronique Anthouard-, Virginie Vico Cristian Del Fabbro23, Michael Alaux, Gabriele Di Gaspero2, Vincent Dum as=, Nicoletta Felice 22, Sophie Paillard=, Irena Jumanz,, Marco Moroldo - Simone Scalabrin=,, Aure lie Canaguier-, Isabelle Le Clainche#, Giorgio Malacrida5 5, Eleonor Durand, Graziano Pesole. 1115, Valerie Laucoul2, Philippe Chatelet23, Didier Merdinoglus Massimo Delledonne l1, Mario Pezzotti 5, 16, Alain Lecharny = Claude Scarpelli, francois Artiguenave M. Enrico Pegs, Giorgio Valle 5, 5, Michele Morgante 2. 5, Michel Caboche 4 Anne-Francoise Adam-Blondon, Jean Weissenbach Francis Quetier-& Patrick Wincker- for The French-Italian Public Consortium for Grapevine Genome Characterization 1z Genoscope(CEA)and UMR 8030 CNRS-Genoscope-Universite dEvry, 2 rue Gaston Cremieux, BP5706, 91057Evry, France. Istituto di Genomica Applicata, Parco scientifico e Tecnologico di Udine, via Linussio 51, 33100 Udine Ital Dipartimento di Matematica ed Informatica, Universita degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy URGV, UMR INRA 1165, CNRS-Universite d' Evry Genomique vegetale, 2 rue Gaston Cremieux, BP5708, 91057 Evry cedex, France. Dipartimento di scienze Agrarie ed Ambientali, Universita degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy CRIBI, Universita degli Studi di Padova, viale G. Colom bo 3, 35121 Padova, Italy URGI, UR1164 Genomique Info, 523, Place des Terrasses, 91034 Evry Cedex, France. UMR INRA 1131, Universite de Strasbourg, Sante de la Vigne et Qualite du Vin, 28 rue de Herrlisheim BP20507, 68021 Colmar France Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, via Celoria 20133 Milano, Italy. Dipartimento di Biochimica e Biologia Molecolare, Universita degli Studi di Bari, via Orabona 4, 70125
Giulia together with a consortium of private companies and banks (IGA). Nature 449, 463-467 (27 September 2007) | doi:10.1038/nature06148; Received 5 April 2007; Accepted 7 August 2007; Published online 26 August 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Olivier Jaillon1,18, Jean-Marc Aury1,18, Benjamin Noel1 , Alberto Policriti2,3 , Christian Clepet4 , Alberto Casagrande2,5 , Nathalie Choisne1,4 , Sébastien Aubourg4 , Nicola Vitulo6,15, Claire Jubin1 , Alessandro Vezzi6,15, Fabrice Legeai7 , Philippe Hugueney8 , Corinne Dasilva1 , David Horner9,15, Erica Mica9,15, Delphine Jublot4 , Julie Poulain1 , Clémence Bruyère4 , Alain Billault1 , Béatrice Segurens1 , Michel Gouyvenoux1 , Edgardo Ugarte1 , Federica Cattonaro2 , Véronique Anthouard1 , Virginie Vico1 , Cristian Del Fabbro2,3 , Michaël Alaux7 , Gabriele Di Gaspero2,5 , Vincent Dumas8 , Nicoletta Felice2,5 , Sophie Paillard4 , Irena Juman2,5 , Marco Moroldo4 , Simone Scalabrin2,3 , Aurélie Canaguier4 , Isabelle Le Clainche4 , Giorgio Malacrida6,15, Eléonore Durand7 , Graziano Pesole10,11,15, Valérie Laucou12, Philippe Chatelet13, Didier Merdinoglu8 , Massimo Delledonne14,15, Mario Pezzotti15,16, Alain Lecharny4 , Claude Scarpelli1 , François Artiguenave1 , M. Enrico Pè9,15, Giorgio Valle6,15, Michele Morgante2,15, Michel Caboche4 , Anne-Françoise Adam-Blondon4 , Jean Weissenbach1 , Francis Quétier1 & Patrick Wincker1 for The French–Italian Public Consortium for Grapevine Genome Characterization 17 1. Genoscope (CEA) and UMR 8030 CNRS-Genoscope-Université d'Evry, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France. 2. Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine, Via Linussio 51, 33100 Udine, Italy. 3. Dipartimento di Matematica ed Informatica, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy. 4. URGV, UMR INRA 1165, CNRS-Université d'Evry Genomique Végétale, 2 rue Gaston Crémieux, BP5708, 91057 Evry cedex, France. 5. Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy. 6. CRIBI, Università degli Studi di Padova, viale G. Colombo 3, 35121 Padova, Italy. 7. URGI, UR1164 Génomique Info, 523, Place des Terrasses, 91034 Evry Cedex, France. 8. UMR INRA 1131, Université de Strasbourg, Santé de la Vigne et Qualité du Vin, 28 rue de Herrlisheim, BP20507, 68021 Colmar, France. 9. Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy. 10. Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Bari, via Orabona 4, 70125 Bari, Italy
Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70125 Bari, Italy. UMR INRA 1097, IRD-Montpellier SupAgro-Univ Montpellier Il, Diversite et Adaptation des plantes Cultivees, 2 Place Pierre Viala, 34060 Montpellier Cedex 1, France. 1098, IRD-Montpellier SupAgro-CIRAD, Developpement et Amelioration des plantes, 2 Place pierre v 4060 Montpellier Cedex 1, France. Dipartimento Scientifico e Tecnologico, Universita degli Studi di verona Strada Le Grazie 15 -Ca Vignal, 37134 Verona, Italy Dipartimento di scienze, Tecnologie e Mercati della vite e del vino, Universita degli Studi di verona, via are c/o Universita degli Studi di siena, via Banchi di sotto 55, 53100 Siena, Italy A list of participants and their affiliations appears at the end of the paper. These authors contributed equally to this work. Corres pendence to d requests for mate rials should be addressed to P.w. m Top of Abstract The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their geneticsl23, These poly ploidization events may have had important consequences in plant evolution in particular for species radiation and adaptation and for the modulation of functional capacities 45.6.B910. Here we eport a high-quality draft of the genome sequence of grapevine( vitis vinifera obtained from a highly homozygous genoty pe. the draft sequen ce of the grapevine genome is the fourth one produced so far for flowering plants, the second for a roody species and the first for a fruit crop(cultivated for both fruit and beverage) Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period1 Several large expansions of gene families with roles in aromatic features are observed. the grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants. Genoscope(CEA)and UMR 8030 CNRS-Genoscope-Universite dEvry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
11. Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70125 Bari, Italy. 12. UMR INRA 1097, IRD-Montpellier SupAgro-Univ. Montpellier II, Diversité et Adaptation des Plantes Cultivées, 2 Place Pierre Viala, 34060 Montpellier Cedex 1, France. 13. UMR INRA 1098, IRD-Montpellier SupAgro-CIRAD, Développement et Amélioration des Plantes, 2 Place Pierre Viala, 34060 Montpellier Cedex 1, France. 14. Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona Strada Le Grazie 15 – Ca’ Vignal, 37134 Verona, Italy. 15. Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, Università degli Studi di Verona, via della Pieve, 70 37029 S. Floriano (VR), Italy. 16. VIGNA-CRA Initiative; Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, c/o Università degli Studi di Siena, via Banchi di Sotto 55, 53100 Siena, Italy. 17. A list of participants and their affiliations appears at the end of the paper. 18. These authors contributed equally to this work. Correspondence to: Correspondence and requests for materials should be addressed to P.W. (Email: pwincker@genoscope.cns.fr). Top of page Abstract The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics1, 2, 3. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities4, 5, 6, 7, 8, 9, 10. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period11. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants. Genoscope (CEA) and UMR 8030 CNRS-Genoscope-Université d'Evry, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France
Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine, Via Linussio 51, 33100 Udine, Italy Dipartimento di Matematica ed Informatica, Universita degli Studi di Udine, via delle Scienze 208 33100 Udine, Italy. URGV, UMR INRA 1165, CNRS-Universite d' Evry genomique Vegetale, 2 rue Gaston Cremieux BP5708, 91057 Evry cedex, France Dipartimento di Scienze Agrarie ed Ambientali, Universita degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy CRIBL, Universita degli Studi di Padova, viale G. Colombo 3, 35 121 Padova, Italy URGI, URI164 Genomique Info, 523, Place des Terrasses, 91034 Evry Cedex, France UMR INRA 1131, Universite de Strasbourg Sante de la Vigne et Qualite du Vin, 28 rue de Herrlisheim. BP20507. 68021 Colmar france Dipartimento di Scienze biomolecolari e Biotecnologie, Universita degli Studi di milano, via Celoria 26, 20133 Milano, Italy Dipartimento di biochimica e Biologia Molecolare, Universita degli Studi di bari, via Orabona 4 70125 Bari, Italy Istituto Tecnologie Biomediche, Consiglio Nazionale delle ricerche, via Amendola 122/D, 70125 UMR INRA 1097, IRD-Montpellier SupAgro-Univ Montpellier Il, Diversite et Adaptation des Plantes Cultivees, 2 Place Pierre Viala, 34060 Montpellier Cedex 1, France UMR INRA 1098, IRD-Montpellier SupAgro-CIRAD, Developpement et Amelioration des Plantes, 2 Place Pierre Viala, 34060 Montpellier Cedex 1, france Dipartimento Scientifico e Tecnologico, Universita degli Studi di verona Strada Le grazie 15 Ca' Vignal, 37134 Verona, Italy Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, Universita degli Studi di Verona, via della Pieve, 70 37029S. Floriano (VR), Italy VIGNA-CRA Initiative; Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, c/o Universita degli Studi di Siena, via Banchi di sotto 55, 53100 Siena, Italy A list of participants and their affiliations appears at the end of the paper These authors contributed equally to this work
Istituto di Genomica Applicata, Parco Scientifico e Tecnologico di Udine, Via Linussio 51, 33100 Udine, Italy. Dipartimento di Matematica ed Informatica, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy. URGV, UMR INRA 1165, CNRS-Université d'Evry Genomique Végétale, 2 rue Gaston Crémieux, BP5708, 91057 Evry cedex, France. Dipartimento di Scienze Agrarie ed Ambientali, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy. CRIBI, Università degli Studi di Padova, viale G. Colombo 3, 35121 Padova, Italy. URGI, UR1164 Génomique Info, 523, Place des Terrasses, 91034 Evry Cedex, France. UMR INRA 1131, Université de Strasbourg, Santé de la Vigne et Qualité du Vin, 28 rue de Herrlisheim, BP20507, 68021 Colmar, France. Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy. Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Bari, via Orabona 4, 70125 Bari, Italy. Istituto Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, via Amendola 122/D, 70125 Bari, Italy. UMR INRA 1097, IRD-Montpellier SupAgro-Univ. Montpellier II, Diversité et Adaptation des Plantes Cultivées, 2 Place Pierre Viala, 34060 Montpellier Cedex 1, France. UMR INRA 1098, IRD-Montpellier SupAgro-CIRAD, Développement et Amélioration des Plantes, 2 Place Pierre Viala, 34060 Montpellier Cedex 1, France. Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona Strada Le Grazie 15 – Ca’ Vignal, 37134 Verona, Italy. Dipartimento di Scienze, Tecnologie e Mercati della Vite e del Vino, Università degli Studi di Verona, via della Pieve, 70 37029 S. Floriano (VR), Italy. VIGNA-CRA Initiative; Consorzio Interuniversitario Nazionale per la Biologia Molecolare delle Piante, c/o Università degli Studi di Siena, via Banchi di Sotto 55, 53100 Siena, Italy. A list of participants and their affiliations appears at the end of the paper. These authors contributed equally to this work