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  • 1
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    The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-04-25
    Description: Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836516/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836516/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ming, Ray -- Hou, Shaobin -- Feng, Yun -- Yu, Qingyi -- Dionne-Laporte, Alexandre -- Saw, Jimmy H -- Senin, Pavel -- Wang, Wei -- Ly, Benjamin V -- Lewis, Kanako L T -- Salzberg, Steven L -- Feng, Lu -- Jones, Meghan R -- Skelton, Rachel L -- Murray, Jan E -- Chen, Cuixia -- Qian, Wubin -- Shen, Junguo -- Du, Peng -- Eustice, Moriah -- Tong, Eric -- Tang, Haibao -- Lyons, Eric -- Paull, Robert E -- Michael, Todd P -- Wall, Kerr -- Rice, Danny W -- Albert, Henrik -- Wang, Ming-Li -- Zhu, Yun J -- Schatz, Michael -- Nagarajan, Niranjan -- Acob, Ricelle A -- Guan, Peizhu -- Blas, Andrea -- Wai, Ching Man -- Ackerman, Christine M -- Ren, Yan -- Liu, Chao -- Wang, Jianmei -- Wang, Jianping -- Na, Jong-Kuk -- Shakirov, Eugene V -- Haas, Brian -- Thimmapuram, Jyothi -- Nelson, David -- Wang, Xiyin -- Bowers, John E -- Gschwend, Andrea R -- Delcher, Arthur L -- Singh, Ratnesh -- Suzuki, Jon Y -- Tripathi, Savarni -- Neupane, Kabi -- Wei, Hairong -- Irikura, Beth -- Paidi, Maya -- Jiang, Ning -- Zhang, Wenli -- Presting, Gernot -- Windsor, Aaron -- Navajas-Perez, Rafael -- Torres, Manuel J -- Feltus, F Alex -- Porter, Brad -- Li, Yingjun -- Burroughs, A Max -- Luo, Ming-Cheng -- Liu, Lei -- Christopher, David A -- Mount, Stephen M -- Moore, Paul H -- Sugimura, Tak -- Jiang, Jiming -- Schuler, Mary A -- Friedman, Vikki -- Mitchell-Olds, Thomas -- Shippen, Dorothy E -- dePamphilis, Claude W -- Palmer, Jeffrey D -- Freeling, Michael -- Paterson, Andrew H -- Gonsalves, Dennis -- Wang, Lei -- Alam, Maqsudul -- R01 GM083873/GM/NIGMS NIH HHS/ -- R01 GM083873-05/GM/NIGMS NIH HHS/ -- R01 LM006845/LM/NLM NIH HHS/ -- R01 LM006845-08/LM/NLM NIH HHS/ -- England -- Nature. 2008 Apr 24;452(7190):991-6. doi: 10.1038/nature06856.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18432245" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Carica/*genetics ; Contig Mapping ; Databases, Genetic ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Molecular Sequence Data ; Plants, Genetically Modified/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/genetics ; Tropical Climate
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    The Sorghum bicolor genome and the diversification of grasses (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-02-04
    Description: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paterson, Andrew H -- Bowers, John E -- Bruggmann, Remy -- Dubchak, Inna -- Grimwood, Jane -- Gundlach, Heidrun -- Haberer, Georg -- Hellsten, Uffe -- Mitros, Therese -- Poliakov, Alexander -- Schmutz, Jeremy -- Spannagl, Manuel -- Tang, Haibao -- Wang, Xiyin -- Wicker, Thomas -- Bharti, Arvind K -- Chapman, Jarrod -- Feltus, F Alex -- Gowik, Udo -- Grigoriev, Igor V -- Lyons, Eric -- Maher, Christopher A -- Martis, Mihaela -- Narechania, Apurva -- Otillar, Robert P -- Penning, Bryan W -- Salamov, Asaf A -- Wang, Yu -- Zhang, Lifang -- Carpita, Nicholas C -- Freeling, Michael -- Gingle, Alan R -- Hash, C Thomas -- Keller, Beat -- Klein, Patricia -- Kresovich, Stephen -- McCann, Maureen C -- Ming, Ray -- Peterson, Daniel G -- Mehboob-ur-Rahman -- Ware, Doreen -- Westhoff, Peter -- Mayer, Klaus F X -- Messing, Joachim -- Rokhsar, Daniel S -- England -- Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA. paterson@uga.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19189423" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Chromosomes, Plant/genetics ; *Evolution, Molecular ; Gene Duplication ; Genes, Plant ; Genome, Plant/*genetics ; Oryza/genetics ; Poaceae/*genetics ; Populus/genetics ; Recombination, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Deletion/genetics ; Sorghum/*genetics ; Zea mays/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-11-13
    Description: Plant genomes, and eukaryotic genomes in general, are typically repetitive, polyploid and heterozygous, which complicates genome assembly. The short read lengths of early Sanger and current next-generation sequencing platforms hinder assembly through complex repeat regions, and many draft and reference genomes are fragmented, lacking skewed GC and repetitive intergenic sequences, which are gaining importance due to projects like the Encyclopedia of DNA Elements (ENCODE). Here we report the whole-genome sequencing and assembly of the desiccation-tolerant grass Oropetium thomaeum. Using only single-molecule real-time sequencing, which generates long (〉16 kilobases) reads with random errors, we assembled 99% (244 megabases) of the Oropetium genome into 625 contigs with an N50 length of 2.4 megabases. Oropetium is an example of a 'near-complete' draft genome which includes gapless coverage over gene space as well as intergenic sequences such as centromeres, telomeres, transposable elements and rRNA clusters that are typically unassembled in draft genomes. Oropetium has 28,466 protein-coding genes and 43% repeat sequences, yet with 30% more compact euchromatic regions it is the smallest known grass genome. The Oropetium genome demonstrates the utility of single-molecule real-time sequencing for assembling high-quality plant and other eukaryotic genomes, and serves as a valuable resource for the plant comparative genomics community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉VanBuren, Robert -- Bryant, Doug -- Edger, Patrick P -- Tang, Haibao -- Burgess, Diane -- Challabathula, Dinakar -- Spittle, Kristi -- Hall, Richard -- Gu, Jenny -- Lyons, Eric -- Freeling, Michael -- Bartels, Dorothea -- Ten Hallers, Boudewijn -- Hastie, Alex -- Michael, Todd P -- Mockler, Todd C -- England -- Nature. 2015 Nov 26;527(7579):508-11. doi: 10.1038/nature15714. Epub 2015 Nov 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA. ; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California 94720, USA. ; Department of Horticulture, Michigan State University, East Lansing, Michigan 48823, USA. ; iPlant Collaborative, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA. ; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou 350002, China. ; IMBIO, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany. ; Pacific Biosciences, Menlo Park, California 94025, USA. ; BioNano Genomics, San Diego, California 92121, USA. ; Ibis Biosciences, Carlsbad, California 92008, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26560029" target="_blank"〉PubMed〈/a〉
    Keywords: Acclimatization/genetics ; Contig Mapping ; Dehydration ; Desiccation ; Droughts ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics ; Molecular Sequence Data ; Poaceae/*genetics ; Sequence Analysis, DNA/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    The banana (Musa acuminata) genome and the evolution of monocotyledonous plants (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-07-18
    Description: Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉D'Hont, Angelique -- Denoeud, France -- Aury, Jean-Marc -- Baurens, Franc-Christophe -- Carreel, Francoise -- Garsmeur, Olivier -- Noel, Benjamin -- Bocs, Stephanie -- Droc, Gaetan -- Rouard, Mathieu -- Da Silva, Corinne -- Jabbari, Kamel -- Cardi, Celine -- Poulain, Julie -- Souquet, Marlene -- Labadie, Karine -- Jourda, Cyril -- Lengelle, Juliette -- Rodier-Goud, Marguerite -- Alberti, Adriana -- Bernard, Maria -- Correa, Margot -- Ayyampalayam, Saravanaraj -- Mckain, Michael R -- Leebens-Mack, Jim -- Burgess, Diane -- Freeling, Mike -- Mbeguie-A-Mbeguie, Didier -- Chabannes, Matthieu -- Wicker, Thomas -- Panaud, Olivier -- Barbosa, Jose -- Hribova, Eva -- Heslop-Harrison, Pat -- Habas, Remy -- Rivallan, Ronan -- Francois, Philippe -- Poiron, Claire -- Kilian, Andrzej -- Burthia, Dheema -- Jenny, Christophe -- Bakry, Frederic -- Brown, Spencer -- Guignon, Valentin -- Kema, Gert -- Dita, Miguel -- Waalwijk, Cees -- Joseph, Steeve -- Dievart, Anne -- Jaillon, Olivier -- Leclercq, Julie -- Argout, Xavier -- Lyons, Eric -- Almeida, Ana -- Jeridi, Mouna -- Dolezel, Jaroslav -- Roux, Nicolas -- Risterucci, Ange-Marie -- Weissenbach, Jean -- Ruiz, Manuel -- Glaszmann, Jean-Christophe -- Quetier, Francis -- Yahiaoui, Nabila -- Wincker, Patrick -- England -- Nature. 2012 Aug 9;488(7410):213-7. doi: 10.1038/nature11241.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre de cooperation Internationale en Recherche Agronomique pour le Developpement, UMR AGAP, F-34398 Montpellier, France. angelique.d'hont@cirad.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22801500" target="_blank"〉PubMed〈/a〉
    Keywords: Conserved Sequence/genetics ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Duplication/genetics ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genotype ; Haploidy ; Molecular Sequence Data ; Musa/classification/*genetics ; Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Architecture and evolution of a minute plant genome (2013)
    Nature Publishing Group (NPG)
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    Publication Date: 2013-05-15
    Description: It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ibarra-Laclette, Enrique -- Lyons, Eric -- Hernandez-Guzman, Gustavo -- Perez-Torres, Claudia Anahi -- Carretero-Paulet, Lorenzo -- Chang, Tien-Hao -- Lan, Tianying -- Welch, Andreanna J -- Juarez, Maria Jazmin Abraham -- Simpson, June -- Fernandez-Cortes, Araceli -- Arteaga-Vazquez, Mario -- Gongora-Castillo, Elsa -- Acevedo-Hernandez, Gustavo -- Schuster, Stephan C -- Himmelbauer, Heinz -- Minoche, Andre E -- Xu, Sen -- Lynch, Michael -- Oropeza-Aburto, Araceli -- Cervantes-Perez, Sergio Alan -- de Jesus Ortega-Estrada, Maria -- Cervantes-Luevano, Jacob Israel -- Michael, Todd P -- Mockler, Todd -- Bryant, Douglas -- Herrera-Estrella, Alfredo -- Albert, Victor A -- Herrera-Estrella, Luis -- 4367/Howard Hughes Medical Institute/ -- England -- Nature. 2013 Jun 6;498(7452):94-8. doi: 10.1038/nature12132. Epub 2013 May 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, 36821 Irapuato, Guanajuato, Mexico.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23665961" target="_blank"〉PubMed〈/a〉
    Keywords: Angiosperms/*genetics ; DNA, Intergenic/genetics ; *Evolution, Molecular ; Gene Duplication/genetics ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Models, Genetic ; Solanum/genetics ; Synteny/genetics ; Vitis/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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