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  • 1
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    Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss [Genetics] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-03-09
    Description: Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5–12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 2
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    The maize rough sheath2 gene and leaf development programs in monocot and dicot plants (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-02
    Description: Leaves of higher plants develop in a sequential manner from the shoot apical meristem. Previously it was determined that perturbed leaf development in maize rough sheath2 (rs2) mutant plants results from ectopic expression of knotted1-like (knox) homeobox genes. Here, the rs2 gene sequence was found to be similar to the Antirrhinum PHANTASTICA (PHAN) gene sequence, which encodes a Myb-like transcription factor. RS2 and PHAN are both required to prevent the accumulation of knox gene products in maize and Antirrhinum leaves, respectively. However, rs2 and phan mutant phenotypes differ, highlighting fundamental differences in monocot and dicot leaf development programs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsiantis, M -- Schneeberger, R -- Golz, J F -- Freeling, M -- Langdale, J A -- GM14578/GM/NIGMS NIH HHS/ -- GM42610/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Apr 2;284(5411):154-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3BR, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10102817" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; DNA-Binding Proteins/chemistry/*genetics ; Down-Regulation ; *Gene Expression Regulation, Plant ; *Genes, Homeobox ; Genes, Plant ; Homeodomain Proteins/*genetics/metabolism ; In Situ Hybridization ; Molecular Sequence Data ; Mutation ; Phenotype ; Plant Development ; Plant Leaves/cytology/genetics/*growth & development/metabolism ; Plant Proteins/chemistry/*genetics ; Plants/*genetics/metabolism ; *Proto-Oncogene Proteins c-myb ; Repressor Proteins/chemistry/*genetics/physiology ; Sequence Alignment ; Zea mays/*genetics/growth & development/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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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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  • 4
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    The Sorghum bicolor genome and the diversification of grasses (2009)
    Nature Publishing Group (NPG)
    Details
    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
    Published by Nature Publishing Group (NPG)
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  • 5
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    Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum (2015)
    Nature Publishing Group (NPG)
    Details
    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
    Published by Nature Publishing Group (NPG)
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  • 6
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    The banana (Musa acuminata) genome and the evolution of monocotyledonous plants (2012)
    Nature Publishing Group (NPG)
    Details
    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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  • 7
    Electronic Resource
    Electronic Resource
    Cell interactions in plants
    Amsterdam : Elsevier
    Current Opinion in Genetics & Development 2 (1992), S. 571-575 
    Details
    ISSN: 0959-437X
    Keywords: [abr] ABP; auxin-binding protein ; [abr] GUS; β-glucuronidase ; [abr] IAA; indole-3-acetic acid ; [abr] SLG; S-locus glycoprotein ; [abr] SRG; S-related genes ; [abr] gIb1; glabrous1 ; [abr] lg1; ligueless1
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0959-437X(05)80174-1
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  • 8
    Electronic Resource
    Electronic Resource
    Purification of maize alcohol dehydrogenase-1 allozymes and comparison of their tryptic peptides
    Amsterdam : Elsevier
    BBA - Protein Structure 624 (1980), S. 102-110 
    Details
    ISSN: 0005-2795
    Keywords: (Maize) ; Alcohol dehydrogenase alloenzyme ; Peptide mapping
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0005-2795(80)90229-9
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  • 9
    Electronic Resource
    Electronic Resource
    Cell interactions in plants
    Amsterdam : Elsevier
    Current Opinion in Genetics & Development 2 (1992), S. 571-575 
    Details
    ISSN: 0959-437X
    Keywords: [abr] ABP; auxin-binding protein ; [abr] GUS; β-glucuronidase ; [abr] IAA; indole-3-acetic acid ; [abr] SLG; S-locus glycoprotein ; [abr] SRG; S-related genes ; [abr] gIb1; glabrous1 ; [abr] lg1; ligueless1
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/S0959-437X(05)80174-1
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  • 10
    Electronic Resource
    Electronic Resource
    Plant Transposable Elements and Insertion Sequences (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Plant Physiology 35 (1984), S. 277-298 
    Details
    ISSN: 0066-4294
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.pp.35.060184.001425
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